archana87@DMED-MJ061MD5:~/NCLscan-1.6$ ./NCLscan.py -c new_NCLscan.config -pj test_NCLscan -o output_last --fq1 simu_5X_100PE_1.fastq --fq2 simu_5X_100PE_1.f astq [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 100000 sequences (10000000 bp)... [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.703 CPU sec, 15.509 real sec [samopen] SAM header is present: 119504 sequences. [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.719 CPU sec, 14.612 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.594 CPU sec, 14.638 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.594 CPU sec, 14.825 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.578 CPU sec, 14.773 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.688 CPU sec, 14.887 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.672 CPU sec, 14.861 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.516 CPU sec, 14.463 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.688 CPU sec, 14.743 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.578 CPU sec, 14.608 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.641 CPU sec, 14.783 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.391 CPU sec, 14.536 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.547 CPU sec, 14.492 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.531 CPU sec, 14.549 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.484 CPU sec, 14.492 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.531 CPU sec, 14.677 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.469 CPU sec, 14.736 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.125 CPU sec, 14.446 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.234 CPU sec, 14.634 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.562 CPU sec, 14.710 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.359 CPU sec, 14.565 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.688 CPU sec, 14.898 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.672 CPU sec, 15.624 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.656 CPU sec, 15.584 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.922 CPU sec, 15.528 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.109 CPU sec, 16.021 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.016 CPU sec, 15.488 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.734 CPU sec, 15.583 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.281 CPU sec, 14.592 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.453 CPU sec, 14.666 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.609 CPU sec, 14.934 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.531 CPU sec, 14.971 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.281 CPU sec, 14.489 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.547 CPU sec, 14.930 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.938 CPU sec, 15.163 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.750 CPU sec, 14.961 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.234 CPU sec, 14.486 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.594 CPU sec, 15.108 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.156 CPU sec, 16.548 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.625 CPU sec, 14.966 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.688 CPU sec, 15.081 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.938 CPU sec, 15.748 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.766 CPU sec, 15.283 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.375 CPU sec, 14.968 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.609 CPU sec, 14.933 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.141 CPU sec, 14.447 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.406 CPU sec, 15.093 real sec [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.828 CPU sec, 18.257 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.828 CPU sec, 17.071 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.859 CPU sec, 16.535 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.797 CPU sec, 17.490 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.062 CPU sec, 17.325 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.000 CPU sec, 17.064 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.672 CPU sec, 16.587 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.688 CPU sec, 16.546 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.969 CPU sec, 16.883 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.078 CPU sec, 17.327 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.281 CPU sec, 16.996 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.875 CPU sec, 17.211 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.984 CPU sec, 17.258 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.969 CPU sec, 17.667 real sec [M::process] read 100000 sequences (10000000 bp)... [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.484 CPU sec, 15.862 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.312 CPU sec, 14.895 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.453 CPU sec, 14.819 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.078 CPU sec, 14.704 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.672 CPU sec, 15.366 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.266 CPU sec, 14.659 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.391 CPU sec, 14.714 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.109 CPU sec, 14.450 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.125 CPU sec, 14.538 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.109 CPU sec, 14.525 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.359 CPU sec, 14.820 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 14.094 CPU sec, 14.633 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.125 CPU sec, 16.237 real sec [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.250 CPU sec, 20.079 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.750 CPU sec, 19.262 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.312 CPU sec, 20.342 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.859 CPU sec, 19.065 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.016 CPU sec, 20.427 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.297 CPU sec, 20.758 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.172 CPU sec, 19.941 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.188 CPU sec, 20.816 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.812 CPU sec, 20.284 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.062 CPU sec, 19.803 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.062 CPU sec, 20.112 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.891 CPU sec, 18.874 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.594 CPU sec, 19.330 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.953 CPU sec, 19.346 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.000 CPU sec, 19.914 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.984 CPU sec, 19.573 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.109 CPU sec, 19.862 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.016 CPU sec, 21.581 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.969 CPU sec, 21.187 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.281 CPU sec, 20.924 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 15.688 CPU sec, 20.193 real sec [M::process] read 100000 sequences (10000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 100000 reads in 16.125 CPU sec, 22.240 real sec [M::process] read 75598 sequences (7559800 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 75598 reads in 12.047 CPU sec, 15.366 real sec [main] Version: 0.7.12-r1039 [main] CMD: /usr/bin/bwa mem -t 1 /home/archana87/NCLscan-1.6/AllRef.fa simu_5X_100PE_1.fastq simu_5X_100PE_1.fastq [main] Real time: 1894.450 sec; CPU: 1458.359 sec # novoalign (AVX2) (V3.09.00 - Build Jun 12 2018 @ 08:54:05) - A short read aligner with qualities. # (C) 2008-2016 Novocraft Technologies Sdn Bhd. # License file: /home/archana87/NCLscan-1.6/novocraft/novoalign.lic # Licensed to University of Saskatchewan # novoalign -r A 1 -n 30 -d /home/archana87/NCLscan-1.6/AllRef.ndx -f output_last/test_NCLscan.main.bwa.unmapped_1.fastq output_last/test_NCLscan.main.bwa.unmapped_2.fastq -o SAM # Starting at Tue Jul 10 10:50:51 2018 # Interpreting input files as Sanger FASTQ. # Index Build Version: 3.9 # Hash length: 14 # Step size: 2 # Paired Reads: 4837799 # Proper Pairs: 28765 ( 0.6%) # Read Sequences: 9675598 # Unique Alignment: 108338 ( 1.1%) # Multi Mapped: 9418822 (97.3%) # No Mapping Found: 148370 ( 1.5%) # QC Failures... # Homopolymer Filter: 68 ( 0.0%) # Timers # Elapsed Time: 37073.473 (secs.) # CPU Time: 709.65 (min.) # Fragment Length Distribution # From To Count # Fragment Distribution is empty. No pairs with MAPQ >= 70. # Done at Tue Jul 10 21:10:31 2018 [samopen] SAM header is present: 119504 sequences. Loaded 3234834689 letters in 297 sequences Searched 914515210 bases in 4703602 sequences Total time cost = 49300.296881 sec PslChimeraFilter v0.4 Loaded 196542248 letters in 95309 sequences Searched 775079204 bases in 3981806 sequences Total time cost = 21193.3517132 sec Loaded 22819188 letters in 23898 sequences Searched 775079204 bases in 3981806 sequences Total time cost = 8157.33763504 sec Loaded 33138 letters in 1 sequences Searched 775079204 bases in 3981806 sequences Total time cost = 27.5838198662 sec JunctionSite2BED v0.3 Reading annotations on chr1. Reading annotations on chr2. Reading annotations on chr3. Reading annotations on chr4. Reading annotations on chr5. Reading annotations on chr6. Reading annotations on chr7. Reading annotations on chr8. Reading annotations on chr9. Reading annotations on chr10. Reading annotations on chr11. Reading annotations on chr12. Reading annotations on chr13. Reading annotations on chr14. Reading annotations on chr15. Reading annotations on chr16. Reading annotations on chr17. Reading annotations on chr18. Reading annotations on chr19. Reading annotations on chr20. Reading annotations on chr21. Reading annotations on chr22. Reading annotations on chrX. Reading annotations on chrY. Reading annotations on chrM. Read 57820 genes, 196520 transcripts and 1196293 exons from the gtf file. # novoindex (3.9) - Universal k-mer index constructor. # (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd # novoindex output_last/test_NCLscan.JS.ndx output_last/test_NCLscan.JS.fa # Creating 4 indexing threads. # Building with 9-mer and step of 1 bp. # novoindex construction dT = 0.2s # Index memory size 0.015Gbyte. # Done. # novoalign (AVX2) (V3.09.00 - Build Jun 12 2018 @ 08:54:05) - A short read aligner with qualities. # (C) 2008-2016 Novocraft Technologies Sdn Bhd. # License file: /home/archana87/NCLscan-1.6/novocraft/novoalign.lic # Licensed to University of Saskatchewan # novoalign -r A 1 -g 99 -x 99 -d output_last/test_NCLscan.JS.ndx -f output_last/test_NCLscan.main.unmapped_1.fastq -o SAM # Starting at Wed Jul 11 21:00:30 2018 # Interpreting input files as Sanger FASTQ. # Index Build Version: 3.9 # Hash length: 9 # Step size: 1 # Read Sequences: 4703602 # Unique Alignment: 14617 ( 0.3%) # Multi Mapped: 15829 ( 0.3%) # No Mapping Found: 4673156 (99.4%) # Timers # Elapsed Time: 364.948 (secs.) # CPU Time: 18.24 (min.) # Done at Wed Jul 11 21:06:35 2018 # novoalign (AVX2) (V3.09.00 - Build Jun 12 2018 @ 08:54:05) - A short read aligner with qualities. # (C) 2008-2016 Novocraft Technologies Sdn Bhd. # License file: /home/archana87/NCLscan-1.6/novocraft/novoalign.lic # Licensed to University of Saskatchewan # novoalign -r A 1 -g 99 -x 99 -d output_last/test_NCLscan.JS.ndx -f output_last/test_NCLscan.main.unmapped_2.fastq -o SAM # Starting at Wed Jul 11 21:06:35 2018 # Interpreting input files as Sanger FASTQ. # Index Build Version: 3.9 # Hash length: 9 # Step size: 1 # Read Sequences: 4703602 # Unique Alignment: 14617 ( 0.3%) # Multi Mapped: 15829 ( 0.3%) # No Mapping Found: 4673156 (99.4%) # Timers # Elapsed Time: 365.691 (secs.) # CPU Time: 18.25 (min.) # Done at Wed Jul 11 21:12:41 2018 End of file reading 4 bytes Total time cost = 0.224915981293 sec End of file reading 4 bytes Total time cost = 0.139180183411 sec PslChimeraFilter v0.4 JunctionSite2BED v0.3 Reading annotations on chr1. Reading annotations on chr2. Reading annotations on chr3. Reading annotations on chr4. Reading annotations on chr5. Reading annotations on chr6. Reading annotations on chr7. Reading annotations on chr8. Reading annotations on chr9. Reading annotations on chr10. Reading annotations on chr11. Reading annotations on chr12. Reading annotations on chr13. Reading annotations on chr14. Reading annotations on chr15. Reading annotations on chr16. Reading annotations on chr17. Reading annotations on chr18. Reading annotations on chr19. Reading annotations on chr20. Reading annotations on chr21. Reading annotations on chr22. Reading annotations on chrX. Reading annotations on chrY. Reading annotations on chrM. Read 57820 genes, 196520 transcripts and 1196293 exons from the gtf file. # novoindex (3.9) - Universal k-mer index constructor. # (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd # novoindex output_last/test_NCLscan.JS2.ndx output_last/test_NCLscan.JS2.fa # Creating 4 indexing threads. # Building with 9-mer and step of 1 bp. # novoindex construction dT = 0.0s # Index memory size 0.001Gbyte. # Done. # novoalign (AVX2) (V3.09.00 - Build Jun 12 2018 @ 08:54:05) - A short read aligner with qualities. # (C) 2008-2016 Novocraft Technologies Sdn Bhd. # License file: /home/archana87/NCLscan-1.6/novocraft/novoalign.lic # Licensed to University of Saskatchewan # novoalign -r A 1 -t 0,1 -d output_last/test_NCLscan.JS2.ndx -f output_last/test_NCLscan.main.unmapped_1.fastq output_last/test_NCLscan.main.unmapped_2.fastq --3Prime -o SAM # Starting at Wed Jul 11 21:14:28 2018 # Interpreting input files as Sanger FASTQ. Error: output_last/test_NCLscan.JS2.ndx does not appear to be a valid novoindex. Code 9 End of file reading 4 bytes Total time cost = 0.161858081818 sec End of file reading 4 bytes Total time cost = 0.0715329647064 sec End of file reading 4 bytes Total time cost = 0.0666210651398 sec End of file reading 4 bytes Total time cost = 0.0526130199432 sec Traceback (most recent call last): File "/home/archana87/NCLscan-1.6/bin/Add_read_count.py", line 118, in add_read_count(args.result_tmp_file, args.result_sam_file, args.output, args.JSParser_bin) File "/home/archana87/NCLscan-1.6/bin/Add_read_count.py", line 13, in add_read_count all_junc_read_with_ref = get_junc_read(result_sam_data, JSParser_bin) File "/home/archana87/NCLscan-1.6/bin/Add_read_count.py", line 66, in get_junc_read junc_read_data = get_read_with_ref(junc_read_sam_data) File "/home/archana87/NCLscan-1.6/bin/Add_read_count.py", line 46, in get_read_with_ref ref_id = re.sub("\.[0-9]*$", "", line[2]) IndexError: list index out of range Traceback (most recent call last): File "/home/archana87/NCLscan-1.6/bin/get_gene_name.py", line 91, in add_gene_name(args.result_tmp_file, args.gene_anno, args.output) File "/home/archana87/NCLscan-1.6/bin/get_gene_name.py", line 8, in add_gene_name result_tmp_data = read_TSV(result_tmp_file) File "/home/archana87/NCLscan-1.6/bin/get_gene_name.py", line 64, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: 'output_last/test_NCLscan.result.tmp2' Traceback (most recent call last): File "./NCLscan.py", line 448, in NCL_Scan4(config, datasets_list, args.project_name, args.output_dir) File "./NCLscan.py", line 255, in NCL_Scan4 final_tmp = read_TSV("{prefix}.result.tmp3".format(**config_options)) File "./NCLscan.py", line 279, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: 'output_last/test_NCLscan.result.tmp3' archana87@DMED-MJ061MD5:~/NCLscan-1.6$ ls AllRef.fa AllRef.ndx GRCh37.p13.genome.fa novocraft RepChrM.fa AllRef.fa.amb bin GRCh37.p13.genome.fa.fai novocraft_new simu_5X_100PE_1.fastq AllRef.fa.ann ChangeLog LICENSE novocraftV3.06.05.Linux3.0.tar.gz simu_5X_100PE_2.fastq AllRef.fa.bwt gencode.v19.annotation.gtf NCLscan.config output UniversityofSaskatchewan.tar.gz AllRef.fa.pac gencode.v19.lncRNA_transcripts.fa NCLscan.py output_last version AllRef.fa.sa gencode.v19.pc_transcripts.fa new_NCLscan.config README.md wget-log archana87@DMED-MJ061MD5:~/NCLscan-1.6$ cd output_last/ archana87@DMED-MJ061MD5:~/NCLscan-1.6/output_last$ du -h * 0 all.test_NCLscan.1b.result 0 all.test_NCLscan.1b.sam 0 all.test_NCLscan.1.result 0 all.test_NCLscan.1.sam 0 all.test_NCLscan.b.result 0 all.test_NCLscan.JS2b.sam 0 all.test_NCLscan.JS2.sam 0 all.test_NCLscan.JS.Parsered.sam 2.8G all.test_NCLscan.JS.sam 0 all.test_NCLscan.result 0 all.test_NCLscan.um3.colinear.psl 0 all.test_NCLscan.um3.fa 0 temp.list 0 test_NCLscan.2b.info 0 test_NCLscan.2.chi.bed 0 test_NCLscan.2.info 0 test_NCLscan.2.info.fa 0 test_NCLscan.2.info.GRCh37.psl 0 test_NCLscan.3b.info 0 test_NCLscan.3.info 0 test_NCLscan.4b.info 0 test_NCLscan.4.info 874M test_NCLscan.chi0.bed 0 test_NCLscan.chi2.bed 0 test_NCLscan.chi3.bed 872M test_NCLscan.chi.bed 128K test_NCLscan.chrM.2.psl 0 test_NCLscan.chrM.um3.psl 17G test_NCLscan.coding.2.psl 0 test_NCLscan.coding.um3.psl 25M test_NCLscan.colinear.psl 0 test_NCLscan.info 0 test_NCLscan.JS1.Idx 0 test_NCLscan.JS1.preIdx 0 test_NCLscan.JS2.cleaned.info 0 test_NCLscan.JS2.fa 0 test_NCLscan.JS2.Idx 0 test_NCLscan.JS2.info 0 test_NCLscan.JS2.info_1 0 test_NCLscan.JS2.info_2 1.1M test_NCLscan.JS2.ndx 0 test_NCLscan.JS2.prefa 0 test_NCLscan.JS2.preIdx 0 test_NCLscan.JS2.result.info 0 test_NCLscan.JS2.seq 0 test_NCLscan.JS2.seq_1 0 test_NCLscan.JS2.seq_2 1.7M test_NCLscan.JS.cleaned.info 0 test_NCLscan.JS.clear.fa 4.0M test_NCLscan.JS.fa 0 test_NCLscan.JS.GRCh37.2.psl 0 test_NCLscan.JS.GRCh37.psl 5.6M test_NCLscan.JS.info 284M test_NCLscan.JS.info_1 229M test_NCLscan.JS.info_2 16M test_NCLscan.JS.ndx 3.9M test_NCLscan.JS.seq 482M test_NCLscan.JS.seq_1 13M test_NCLscan.JS.seq12 417M test_NCLscan.JS.seq_2 0 test_NCLscan.linearJS 2.3G test_NCLscan.lncRNA.2.psl 0 test_NCLscan.lncRNA.um3.psl 1.4G test_NCLscan.main_1.JS.sam 0 test_NCLscan.main_1.um3.fastq 1.4G test_NCLscan.main_2.JS.sam 0 test_NCLscan.main_2.um3.fastq 1.2G test_NCLscan.main.bwa.bam 1.3G test_NCLscan.main.bwa.unmapped_1.fastq 1.3G test_NCLscan.main.bwa.unmapped_2.fastq 6.9G test_NCLscan.main.bwa.unmapped.sam 308M test_NCLscan.main.bwa.unmapped.sam.id 0 test_NCLscan.main.JS2b.sam 0 test_NCLscan.main.JS2.sam 3.7G test_NCLscan.main.sam 0 test_NCLscan.main.um3.fa 1.2G test_NCLscan.main.unmapped_1.fastq 1.2G test_NCLscan.main.unmapped_2.fastq 1.2G test_NCLscan.main.unmapped.fa 3.5G test_NCLscan.main.unmapped.sam 299M test_NCLscan.main.unmapped.sam.id 0 test_NCLscan.ncl.sam 0 test_NCLscan.PreJS2.bed 0 test_NCLscan.PreJS2.info 0 test_NCLscan.PreJS2.info2 0 test_NCLscan.PreJS2.seq 0 test_NCLscan.PreJS2.seq2 800M test_NCLscan.preJS.bed 748M test_NCLscan.preJS.info 493M test_NCLscan.preJS.info2 1.2G test_NCLscan.preJS.seq 898M test_NCLscan.preJS.seq2 0 test_NCLscan.preResult 0 test_NCLscan.result.info 0 test_NCLscan.result.sam 0 test_NCLscan.result.tmp 2.4G test_NCLscan.rG.non_un.psl 4.1G test_NCLscan.rG.psl 0 test_NCLscan.rG.um3.psl 0 test_NCLscan.tmp2.info 0 test_NCLscan.tmp.info 1011M test_NCLscan.unmapped.2.fa 1.2G test_NCLscan.unmapped.fa 265M test_NCLscan.un.psl 0 tmp.info