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KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
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ERROR: NO COMMON CONTIGS FOUND BETWEEN THE BAM FILE AND THE FASTA FILE #18

Closed bo8883 closed 2 years ago

bo8883 commented 2 years ago

I followed the directions exactly but I get this error. Do you know what's going wrong? Thanks.

bash-4.2$ singularity exec --bind $HD_DIR hapdup_0.6.sif hapdup --assembly $HD_DIR/assembly.fasta --bam $HD_DIR/lr_mapping.bam --out-dir $HD_DIR/hapdup -t 64 --rtype ont INFO: Converting SIF file to temporary sandbox... [2022-06-23 13:01:10] INFO: Skipped filtering phase [2022-06-23 13:01:10] INFO: Running: pepper_variant call_variant -b /home/bozhou/src/hapdup/filtered.bam -f /home/bozhou/src/assembly.fasta -o /home/bozhou/src/hapdup/pepper -m /home/bozhou/src/hapdup/pepper/pepper_model.bin -t 64 -s Sample --ont_r9_guppy5_sup --include-supplementary --no_quantized 2>&1 |tee /home/bozhou/src/hapdup/pepper/pepper.log [06-23-2022 13:01:11] INFO: ONT VARIANT CALLING MODE SELECTED. [06-23-2022 13:01:11] INFO: MODE: PEPPER SNP [06-23-2022 13:01:11] INFO: THRESHOLDS ARE SET TO: [06-23-2022 13:01:11] INFO: MIN MAPQ: 5 [06-23-2022 13:01:11] INFO: MIN SNP BASEQ: 1 [06-23-2022 13:01:11] INFO: MIN INDEL BASEQ: 1 [06-23-2022 13:01:11] INFO: MIN SNP FREQUENCY: 0.1 [06-23-2022 13:01:11] INFO: MIN INSERT FREQUENCY: 0.15 [06-23-2022 13:01:11] INFO: MIN DELETE FREQUENCY: 0.15 [06-23-2022 13:01:11] INFO: MIN COVERAGE THRESHOLD: 3 [06-23-2022 13:01:11] INFO: MIN CANDIDATE SUPPORT: 2 [06-23-2022 13:01:11] INFO: MIN SNP CANDIDATE FREQUENCY: 0.1 [06-23-2022 13:01:11] INFO: MIN INDEL CANDIDATE FREQUENCY: 0.1 [06-23-2022 13:01:11] INFO: SKIP INDEL CANDIDATES: False [06-23-2022 13:01:11] INFO: MAX ALLOWED CANDIDATE IN ONE SITE: 4 [06-23-2022 13:01:11] INFO: MIN SNP PREDICTIVE VALUE: 0.1 [06-23-2022 13:01:11] INFO: MIN INSERT PREDICTIVE VALUE: 0.25 [06-23-2022 13:01:11] INFO: MIN DELETE PREDICTIVE VALUE: 0.25 [06-23-2022 13:01:11] INFO: SNP QV CUTOFF FOR RE-GENOTYPING: 15 [06-23-2022 13:01:11] INFO: INDEL QV CUTOFF FOR RE-GENOTYPING: 10 [06-23-2022 13:01:11] INFO: REPORT ALL SNPs ABOVE THRESHOLD: 0 [06-23-2022 13:01:11] INFO: REPORT ALL INDELs ABOVE THRESHOLD: 0 [06-23-2022 13:01:11] INFO: CALL VARIANT MODULE SELECTED [06-23-2022 13:01:11] INFO: RUN-ID: 06232022_130111 [06-23-2022 13:01:11] INFO: IMAGE OUTPUT: /home/bozhou/src/hapdup/pepper/images_06232022_130111/ [06-23-2022 13:01:11] INFO: STEP 1/3 GENERATING IMAGES: [06-23-2022 13:01:11] ERROR: NO COMMON CONTIGS FOUND BETWEEN THE BAM FILE AND THE FASTA FILE.rm: cannot remove '/home/bozhou/src/hapdup/pepper/images': No such file or directory rm: cannot remove '/home/bozhou/src/hapdup/pepper/predictions': No such file or directory [2022-06-23 13:01:11] ERROR: Missing output: /home/bozhou/src/hapdup/pepper/PEPPER_VARIANT_FULL.vcf Traceback (most recent call last): File "/usr/local/bin/hapdup", line 8, in sys.exit(main()) File "/usr/local/lib/python3.8/dist-packages/hapdup/main.py", line 183, in main file_check(pepper_vcf) File "/usr/local/lib/python3.8/dist-packages/hapdup/main.py", line 110, in file_check raise Exception("Missing output") Exception: Missing output INFO: Cleaning up image...

bo8883 commented 2 years ago

okay, I figured it out; need to remove the filtered.bam file

Axze-rgb commented 4 months ago

Hello, I am having the same issue and I don't understand the solution. Should I remove the filter bam and relaunch HapDup at another point in the pipeline? How do I do that? Thanks

bo8883 commented 4 months ago

If I remember correctly, there was already a filter.bam file in the directory, and that needs to be removed before restarting. Sorry, I could be wrong, but it's been a while.

Axze-rgb commented 4 months ago

No worries I restarted everything from the mapping of long reads on the assembly and it worked. It doesn't make any sense but I got my phased assembly.