Job ID = 14167168 SRX = SRX10340466 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 858498 READS because READLEN < 1 Read 7223505 spots for SRR13962475/SRR13962475.sra Written 7223505 spots for SRR13962475/SRR13962475.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167703 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 4 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 7 unmatched pairs [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1575952 / 5324079 = 0.2960 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Dec 2021 11:00:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:47: 1000000 INFO @ Fri, 10 Dec 2021 11:00:56: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:01:06: 3000000 INFO @ Fri, 10 Dec 2021 11:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Dec 2021 11:01:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:01:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:01:17: 4000000 INFO @ Fri, 10 Dec 2021 11:01:18: 1000000 INFO @ Fri, 10 Dec 2021 11:01:28: 5000000 INFO @ Fri, 10 Dec 2021 11:01:29: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:01:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Dec 2021 11:01:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:01:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:01:39: 6000000 INFO @ Fri, 10 Dec 2021 11:01:40: 3000000 INFO @ Fri, 10 Dec 2021 11:01:47: 1000000 INFO @ Fri, 10 Dec 2021 11:01:50: 7000000 INFO @ Fri, 10 Dec 2021 11:01:51: 4000000 INFO @ Fri, 10 Dec 2021 11:01:57: 2000000 INFO @ Fri, 10 Dec 2021 11:02:01: 8000000 INFO @ Fri, 10 Dec 2021 11:02:02: 5000000 INFO @ Fri, 10 Dec 2021 11:02:05: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:02:05: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:02:05: #1 total tags in treatment: 3619344 INFO @ Fri, 10 Dec 2021 11:02:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:02:05: #1 tags after filtering in treatment: 3533448 INFO @ Fri, 10 Dec 2021 11:02:05: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:02:05: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:05: #2 number of paired peaks: 621 WARNING @ Fri, 10 Dec 2021 11:02:05: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Fri, 10 Dec 2021 11:02:05: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:05: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:05: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:05: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:05: #2 predicted fragment length is 231 bps INFO @ Fri, 10 Dec 2021 11:02:05: #2 alternative fragment length(s) may be 231 bps INFO @ Fri, 10 Dec 2021 11:02:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.05_model.r WARNING @ Fri, 10 Dec 2021 11:02:05: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:05: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Fri, 10 Dec 2021 11:02:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:02:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:02:07: 3000000 INFO @ Fri, 10 Dec 2021 11:02:12: 6000000 INFO @ Fri, 10 Dec 2021 11:02:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:02:17: 4000000 INFO @ Fri, 10 Dec 2021 11:02:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:02:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.05_summits.bed INFO @ Fri, 10 Dec 2021 11:02:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2017 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:02:24: 7000000 INFO @ Fri, 10 Dec 2021 11:02:26: 5000000 INFO @ Fri, 10 Dec 2021 11:02:35: 8000000 INFO @ Fri, 10 Dec 2021 11:02:36: 6000000 INFO @ Fri, 10 Dec 2021 11:02:38: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:02:38: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:02:38: #1 total tags in treatment: 3619344 INFO @ Fri, 10 Dec 2021 11:02:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:02:38: #1 tags after filtering in treatment: 3533448 INFO @ Fri, 10 Dec 2021 11:02:38: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:02:38: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:39: #2 number of paired peaks: 621 WARNING @ Fri, 10 Dec 2021 11:02:39: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Fri, 10 Dec 2021 11:02:39: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:39: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:39: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:39: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:39: #2 predicted fragment length is 231 bps INFO @ Fri, 10 Dec 2021 11:02:39: #2 alternative fragment length(s) may be 231 bps INFO @ Fri, 10 Dec 2021 11:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.10_model.r WARNING @ Fri, 10 Dec 2021 11:02:39: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:39: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Fri, 10 Dec 2021 11:02:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:02:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:02:45: 7000000 INFO @ Fri, 10 Dec 2021 11:02:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.10_summits.bed INFO @ Fri, 10 Dec 2021 11:02:50: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (797 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:02:53: 8000000 INFO @ Fri, 10 Dec 2021 11:02:56: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:02:56: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:02:56: #1 total tags in treatment: 3619344 INFO @ Fri, 10 Dec 2021 11:02:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:02:56: #1 tags after filtering in treatment: 3533448 INFO @ Fri, 10 Dec 2021 11:02:56: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:02:56: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:56: #2 number of paired peaks: 621 WARNING @ Fri, 10 Dec 2021 11:02:56: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Fri, 10 Dec 2021 11:02:56: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:56: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:56: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:56: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:56: #2 predicted fragment length is 231 bps INFO @ Fri, 10 Dec 2021 11:02:56: #2 alternative fragment length(s) may be 231 bps INFO @ Fri, 10 Dec 2021 11:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.20_model.r WARNING @ Fri, 10 Dec 2021 11:02:56: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:56: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Fri, 10 Dec 2021 11:02:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:02:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:03:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340466/SRX10340466.20_summits.bed INFO @ Fri, 10 Dec 2021 11:03:08: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (276 records, 4 fields): 2 millis CompletedMACS2peakCalling