Could not find conda environment: cutruntools2 You can list all discoverable environments with `conda info --envs`. ==================================== Bulk data analysis pipeline will run ============================================================== ## Input FASTQ folder: /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CutNRun_6-18-21/human ## Sample name: SL_04_S4 ## Workdir folder: /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CutNRun_6-18-21/SL_04_S4 ## Experiment name: SL_04_S4 ## Experiment type: CUT&RUN ## Reference genome: hg38 ## Spike-in genome: FALSE ## Spike-in normalization: FALSE ## Fragment 120 filtration: TRUE ================================================================================================================================= [info] Input file is SL_04_S4_R1_001.fastq.gz and SL_04_S4_R2_001.fastq.gz Thu Jul 8 17:55:21 EDT 2021 [info] Trimming file SL_04_S4 ... Thu Jul 8 17:55:21 EDT 2021 [info] Second stage trimming SL_04_S4 ... Thu Jul 8 18:11:25 EDT 2021 [info] Aligning file SL_04_S4 to reference genome... Thu Jul 8 18:23:32 EDT 2021 [info] Bowtie2 command: --dovetail --phred33 [info] The dovetail mode is enabled [as parameter frag_120 is on] [info] FASTQ files won't be aligned to the spike-in genome [info] Filtering unmapped fragments... SL_04_S4.bam Thu Jul 8 18:34:51 EDT 2021 [info] Sorting BAM... SL_04_S4.bam Thu Jul 8 18:36:47 EDT 2021 INFO 2021-07-08 18:36:48 SortSam ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** SortSam -INPUT sorted/SL_04_S4.step1.bam -OUTPUT sorted/SL_04_S4.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY SILENT ********** 18:36:49.092 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install/picard-2.8.0.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Jul 08 18:36:49 EDT 2021] SortSam INPUT=sorted/SL_04_S4.step1.bam OUTPUT=sorted/SL_04_S4.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=SILENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Thu Jul 08 18:36:49 EDT 2021] Executing as f0042dk@n02.hpcc.dartmouth.edu on Linux 3.10.0-1160.31.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_292-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.21.7-SNAPSHOT INFO 2021-07-08 18:36:49 SortSam Seen many non-increasing record positions. Printing Read-names as well. INFO 2021-07-08 18:37:21 SortSam Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 32s. Last read position: chr4:174,843,229. Last read name: NB501031:621:HWYF2AFX2:2:11311:25711:7823 INFO 2021-07-08 18:37:55 SortSam Read 20,000,000 records. Elapsed time: 00:01:05s. Time for last 10,000,000: 33s. Last read position: chr1:19,153,505. Last read name: NB501031:621:HWYF2AFX2:3:21612:11919:16901 INFO 2021-07-08 18:38:18 SortSam Finished reading inputs, merging and writing to output now. INFO 2021-07-08 18:39:51 SortSam Wrote 10,000,000 records from a sorting collection. Elapsed time: 00:03:01s. Time for last 10,000,000: 92s. Last read position: chr18:1,909,991 INFO 2021-07-08 18:41:22 SortSam Wrote 20,000,000 records from a sorting collection. Elapsed time: 00:04:32s. Time for last 10,000,000: 91s. Last read position: chr6:10,694,018 [Thu Jul 08 18:42:24 EDT 2021] picard.sam.SortSam done. Elapsed time: 5.59 minutes. Runtime.totalMemory()=10351542272 [info] Marking duplicates... SL_04_S4.bam Thu Jul 8 18:42:25 EDT 2021 [info] Removing duplicates... SL_04_S4.bam Thu Jul 8 18:50:15 EDT 2021 [info] Filtering to <120bp... dup.marked and dedup BAMs Thu Jul 8 18:52:15 EDT 2021 [info] Creating bam index files... SL_04_S4.bam Thu Jul 8 18:53:11 EDT 2021 [info] Reads shifting Thu Jul 8 18:53:15 EDT 2021 [info] Your data won't be shifted as the experiment_type is specified as CUT&RUN... [info] Peak calling using MACS2... SL_04_S4.bam [info] Logs are stored in /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CutNRun_6-18-21/SL_04_S4/logs Thu Jul 8 18:53:15 EDT 2021 [info] Peak calling with BAM file with NO duplications [info] macs2 narrow peak calling [info] macs2 broad peak calling [info] Getting broad peak summits [info] SEACR stringent peak calling Calling enriched regions without control file Proceeding without normalization of control to experimental bedgraph Using stringent threshold Creating experimental AUC file: Thu Jul 8 18:54:24 EDT 2021 Calculating optimal AUC threshold: Thu Jul 8 18:54:24 EDT 2021 Using user-provided threshold: Thu Jul 8 18:54:24 EDT 2021 Creating thresholded feature file: Thu Jul 8 18:54:28 EDT 2021 Empirical false discovery rate = 0.01 Merging nearby features and eliminating control-enriched features: Thu Jul 8 18:54:28 EDT 2021 Removing temporary files: Thu Jul 8 18:54:28 EDT 2021 Done: Thu Jul 8 18:54:28 EDT 2021 [info] Generating the normalized signal file with BigWig format... Thu Jul 8 18:54:28 EDT 2021 [info] Your bigwig file won't be normalized with spike-in reads [info] Input file is /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CutNRun_6-18-21/SL_04_S4/peakcalling/macs2.narrow/SL_04_S4_peaks.narrowPeak [info] Get randomized [1000] peaks from the top [2000] peaks... [info] Filtering the blacklist regions for the selected peak files [info] Getting Fasta sequences Warning: the index file is older than the FASTA file. Feature (chrUn_KI270438v1:112311-112512) beyond the length of chrUn_KI270438v1 size (112505 bp). Skipping. [info] Start MEME analysis for de novo motif finding ... [info] Up to 10 will be output ... Log::Log4perl configuration looks suspicious: No loggers defined at /dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/meme/lib/site_perl/5.26.2/Log/Log4perl/Config.pm line 325. Starting getsize: getsize random1000/MEME_SL_04_S4_shuf/SL_04_S4_summits_padded.fa 1> $metrics /dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/meme/libexec/meme-5.0.2/getsize: error while loading shared libraries: libicui18n.so.58: cannot open shared object file: No such file or directory getsize exited with error code 127 getsize failed me... at /dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/meme/bin/meme-chip line 748. [info] De Novo motifs can be found: random1000/MEME_SL_04_S4_shuf ... [info] Loading the De Novo motifs ... Traceback (most recent call last): File "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install/read.meme.py", line 92, in ss = read_summary(this_dir + "/summary.tsv") File "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install/read.meme.py", line 7, in read_summary f = open(n) FileNotFoundError: [Errno 2] No such file or directory: 'random1000/MEME_SL_04_S4_shuf/summary.tsv' [info] The signficance cutoff of Fimo scaning is 0.0005... [info] Motif files can be found: random1000/MEME_SL_04_S4_shuf/motifs [info] Filtering the blacklist regions for the selected peak files [info] Getting Fasta sequences Warning: the index file is older than the FASTA file. [info] Scaning the De Novo motifs for each peak ls: cannot access 'random1000/MEME_SL_04_S4_shuf/motifs': No such file or directory [info] Output can be found: fimo.result/SL_04_S4 # # Congrats! The bulk data analysis is complete! # --------------------------------------------------------------------------