[ERROR] No full-alignment output for file with Docker Dockerfile

[littleisland8]

Hi,

I installed Clair3 with the option N 5 of the Installation section (Docker Dockerfile). However, when I run Clair3 with these parameters:
docker run -it -v ${INPUT_DIR}:${INPUT_DIR} -v ${OUTPUT_DIR}:${OUTPUT_DIR} hkubal/clair3:latest /opt/bin/run_clair3.sh --bam_fn=${INPUT_DIR}/sample.srt.bam --ref_fn=${INPUT_DIR}/ref.fa --bed_fn=${INPUT_DIR}/target.bed --snp_min_af=0.05 --indel_min_af=0.05 --enable_long_indel --threads=${THREADS} --platform="ont" --model_path="/opt/models/${MODEL_NAME}" --output=${OUTPUT_DIR}

I got the error: [ERROR] No full-alignment output for file

in the issue section there is a similar problem (#181) resolved by hkubal/clair3:latest. However I already put hkubal/clair3:latest in the command line.

How can I fix this issue?

[aquaskyline]

Please send us your log file.

[littleisland8]

Find attached the run_clair3.log and all the log files generated in the log dir. I remain at disposal for any further information Kind regards Il giorno sab 9 set 2023 alle ore 15:56 Ruibang Luo < ***@***.***> ha scritto:

…

Please send us your log file. — Reply to this email directly, view it on GitHub <#225 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AN5Z2HDVVHXAELQ6GUJHKC3XZRYQ5ANCNFSM6AAAAAA4NBXZLU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Simone Romagnoli - PhD Dept. of Experimental and Clinical Medicine University of Florence Area degli allegati

[chdews]

Hi,
I had the same problem, How can I fix this issue?

[chdews]

hello,
this is my log

[INFO] CLAIR3 VERSION: v1.0.4
[INFO] BAM FILE PATH: /home/minit/Project/snakemake_data/3/mm2/bam/bacteria03_100000_viruses.bam
[INFO] REFERENCE FILE PATH: /home/minit/Project/date/Reference/viruses.fa
[INFO] MODEL PATH: /home/minit/Project/minit/Clair3-1/models/ont_guppy5
[INFO] OUTPUT FOLDER: /home/minit/Project/Clair3/clair3.vcf
[INFO] PLATFORM: ont
[INFO] THREADS: 6
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: EMPTY
[INFO] CONDA PREFIX: /home/minit/archiconda3/envs/Snakemake
[INFO] SAMTOOLS PATH: samtools
[INFO] PYTHON PATH: python3
[INFO] PYPY PATH: pypy3
[INFO] PARALLEL PATH: parallel
[INFO] WHATSHAP PATH: whatshap
[INFO] LONGPHASE PATH: EMPTY
[INFO] CHUNK SIZE: 5000000
[INFO] FULL ALIGN PROPORTION: 0.7
[INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
[INFO] PHASING PROPORTION: 0.8
[INFO] MINIMUM MQ: 5
[INFO] MINIMUM COVERAGE: 2
[INFO] SNP AF THRESHOLD: 0.08
[INFO] INDEL AF THRESHOLD: 0.15
[INFO] ENABLE FILEUP ONLY CALLING: False
[INFO] ENABLE FAST MODE CALLING: False
[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
[INFO] ENABLE PRINTING REFERENCE CALLS: False
[INFO] ENABLE OUTPUT GVCF: False
[INFO] ENABLE HAPLOID PRECISE MODE: False
[INFO] ENABLE HAPLOID SENSITIVE MODE: False
[INFO] ENABLE INCLUDE ALL CTGS CALLING: True
[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: False
[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
[INFO] ENABLE LONG INDEL CALLING: False
[INFO] ENABLE C_IMPLEMENT: True

+ /home/minit/Project/Clair3/scripts/clair3_c_impl.sh --bam_fn /home/minit/Project/snakemake_data/3/mm2/bam/bacteria03_100000_viruses.bam --ref_fn /home/minit/Project/date/Reference/viruses.fa --threads 6 --model_path /home/minit/Project/minit/Clair3-1/models/ont_guppy5 --platform ont --output /home/minit/Project/Clair3/clair3.vcf --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=EMPTY --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.8 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=2 --min_contig_size=0 --pileup_only=False --gvcf=False --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=True --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=False --longphase=EMPTY --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=False --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False

[INFO] Check environment variables
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/log
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/pileup_output
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/merge_output
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/phase_output
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/gvcf_tmp_output
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/full_alignment_output
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/phase_output/phase_vcf
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/phase_output/phase_bam
[INFO] Create folder /home/minit/Project/Clair3/clair3.vcf/tmp/full_alignment_output/candidate_bed
[INFO] --include_all_ctgs enabled
�[93m[WARNING] Please enable --no_phasing_for_fa if calling variant in non-diploid organisms�[0m
[INFO] Call variant in contigs: NC_004718.3 NC_028752.1 NC_006213.1 NC_045512.2
[INFO] Chunk number for each contig: 1 1 1 1
�[93m[WARNING] Current maximum contig length 196858 is much smaller than default chunk size 5000000, You may set a smaller chunk size by setting --chunk_size=$ for better parallelism.�[0m
[INFO] 1/7 Call variants using pileup model
Calling variants ...
Total processed positions in NC_004718.3 (chunk 1/1) : 0
Total time elapsed: 0.03 s
[INFO] No vcf output for file /home/minit/Project/Clair3/clair3.vcf/tmp/pileup_output/pileup_NC_004718.3_1.vcf, remove empty file
Calling variants ...
Total processed positions in NC_028752.1 (chunk 1/1) : 324
Total time elapsed: 18.08 s
Calling variants ...
Total processed positions in NC_006213.1 (chunk 1/1) : 452
Total time elapsed: 18.89 s
Calling variants ...
Total processed positions in NC_045512.2 (chunk 1/1) : 212
Total time elapsed: 26.72 s

real	0m38.365s
user	1m39.915s
sys	0m8.024s

[INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
[INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 5
[INFO] Total heterozygous SNP positions selected: NC_004718.3: 0
[INFO] Total heterozygous SNP positions selected: NC_028752.1: 5
[INFO] Total heterozygous SNP positions selected: NC_006213.1: 6
[INFO] Total heterozygous SNP positions selected: NC_045512.2: 6

real	0m1.324s
user	0m2.656s
sys	0m0.797s

[INFO] 3/7 Phase VCF file using Whatshap
This is WhatsHap 2.0 running under Python 3.8.6
Working on 1 sample from 1 family

# Resource usage
Maximum memory usage: 0.048 GB
Time spent reading BAM/CRAM:                    0.0 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     0.0 s
Time spent phasing:                             0.0 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.0 s
Total elapsed time:                             0.0 s
This is WhatsHap 2.0 running under Python 3.8.6
Working on 1 sample from 1 family

# Working on contig NC_006213.1 in individual SAMPLE
Found 6 usable heterozygous variants (0 skipped due to missing genotypes)
Found 17 reads covering 6 variants
Kept 2 reads that cover at least two variants each
Selected 2 most phase-informative reads covering 2 variants
Phasing 1 sample by solving the MEC problem ...
Largest block contains 2 variants (100.0% of accessible variants) between position 13666 and 13706

# Resource usage
Maximum memory usage: 0.049 GB
Time spent reading BAM/CRAM:                    0.0 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     0.0 s
Time spent phasing:                             0.0 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.0 s
Total elapsed time:                             0.0 s
This is WhatsHap 2.0 running under Python 3.8.6
Working on 1 sample from 1 family

# Working on contig NC_028752.1 in individual SAMPLE
Found 5 usable heterozygous variants (0 skipped due to missing genotypes)
Found 8 reads covering 5 variants
Kept 3 reads that cover at least two variants each
Selected 3 most phase-informative reads covering 2 variants
Phasing 1 sample by solving the MEC problem ...
Largest block contains 2 variants (100.0% of accessible variants) between position 115 and 117

# Resource usage
Maximum memory usage: 0.049 GB
Time spent reading BAM/CRAM:                    0.0 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     0.0 s
Time spent phasing:                             0.0 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.0 s
Total elapsed time:                             0.0 s
This is WhatsHap 2.0 running under Python 3.8.6
Working on 1 sample from 1 family

# Working on contig NC_045512.2 in individual SAMPLE
Found 6 usable heterozygous variants (0 skipped due to missing genotypes)
Found 2081 reads covering 6 variants
Kept 5 reads that cover at least two variants each
Selected 5 most phase-informative reads covering 4 variants
Phasing 1 sample by solving the MEC problem ...
Largest block contains 2 variants (50.0% of accessible variants) between position 9198 and 9953

# Resource usage
Maximum memory usage: 0.050 GB
Time spent reading BAM/CRAM:                    6.2 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     0.0 s
Time spent phasing:                             0.0 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.0 s
Total elapsed time:                             6.2 s

real	0m8.587s
user	0m12.851s
sys	0m1.401s

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 15.0
[INFO] Set reference calls quality cutoff 11.0
�[93m[WARNING] Cannot find any low-quality 0/0, 0/1 or 1/1 variant in pileup output in contig NC_004718.3�[0m
�[93m[WARNING] Copying pileup.vcf.gz to /home/minit/Project/Clair3/clair3.vcf/merge_output.vcf.gz�[0m
[INFO] Low quality reference calls to be processed in NC_004718.3: 0
[INFO] Low quality variants to be processed in NC_004718.3: 0
[INFO] Low quality reference calls to be processed in NC_028752.1: 41
[INFO] Low quality variants to be processed in NC_028752.1: 121
[INFO] Low quality reference calls to be processed in NC_006213.1: 32
[INFO] Low quality variants to be processed in NC_006213.1: 5
[INFO] Low quality reference calls to be processed in NC_045512.2: 5
[INFO] Low quality variants to be processed in NC_045512.2: 6

real	0m1.338s
user	0m2.708s
sys	0m0.813s

[INFO] 6/7 Call low-quality variants using full-alignment model
Calling variants ...
Total processed positions in  : 0
�[91m[ERROR] No full-alignment output for file //home/minit/Project/Clair3/clair3.vcf/tmp/full_alignment_output/full_alignment_.vcf�[0m
Total time elapsed: 0.02 s
[INFO] No vcf output for file /home/minit/Project/Clair3/clair3.vcf/tmp/full_alignment_output/full_alignment_.vcf, remove empty file
Calling variants ...
Total processed positions in NC_006213.1 (chunk 1/1) : 37
Total time elapsed: 6.38 s
Calling variants ...
Total processed positions in NC_045512.2 (chunk 1/1) : 11
Total time elapsed: 7.45 s
Calling variants ...
Total processed positions in NC_028752.1 (chunk 1/1) : 162
Total time elapsed: 10.93 s

real	0m22.775s
user	1m1.637s
sys	0m7.441s

[INFO] 7/7 Merge pileup VCF and full-alignment VCF
[INFO] Pileup variants processed in NC_004718.3: 0
[INFO] Full-alignment variants processed in NC_004718.3: 0
[INFO] Pileup variants processed in NC_028752.1: 20
[INFO] Full-alignment variants processed in NC_028752.1: 117
[INFO] Pileup variants processed in NC_006213.1: 1
[INFO] Full-alignment variants processed in NC_006213.1: 2
[INFO] Pileup variants processed in NC_045512.2: 37
[INFO] Full-alignment variants processed in NC_045512.2: 3

real	0m1.502s
user	0m3.066s
sys	0m1.170s

[INFO] Finish calling, output file: /home/minit/Project/Clair3/clair3.vcf/merge_output.vcf.gz

real	1m21.209s
user	3m8.392s
sys	0m21.567s

[aquaskyline]

As long as you can get merge_output.vcf.gz, please ignore the error message [ERROR] No full-alignment output for file. In the next version we will change the prompt to avoid misunderstandings.

[aquaskyline]

fixed in v1.0.5