Job ID = 8069395 SRX = SRX7217789 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:59 prefetch.2.10.7: 1) Downloading 'SRR10533866'... 2020-08-08T03:31:59 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:35 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:35 prefetch.2.10.7: 1) 'SRR10533866' was downloaded successfully 2020-08-08T03:34:35 prefetch.2.10.7: 'SRR10533866' has 0 unresolved dependencies Read 7699591 spots for SRR10533866/SRR10533866.sra Written 7699591 spots for SRR10533866/SRR10533866.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070368 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:11 7699591 reads; of these: 7699591 (100.00%) were paired; of these: 1571767 (20.41%) aligned concordantly 0 times 5221253 (67.81%) aligned concordantly exactly 1 time 906571 (11.77%) aligned concordantly >1 times ---- 1571767 pairs aligned concordantly 0 times; of these: 508982 (32.38%) aligned discordantly 1 time ---- 1062785 pairs aligned 0 times concordantly or discordantly; of these: 2125570 mates make up the pairs; of these: 1881031 (88.50%) aligned 0 times 127745 (6.01%) aligned exactly 1 time 116794 (5.49%) aligned >1 times 87.78% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 945902 / 6593558 = 0.1435 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sat, 08 Aug 2020 12:55:14: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:14: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:23: 1000000 INFO @ Sat, 08 Aug 2020 12:55:32: 2000000 INFO @ Sat, 08 Aug 2020 12:55:40: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sat, 08 Aug 2020 12:55:44: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:44: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:50: 4000000 INFO @ Sat, 08 Aug 2020 12:55:55: 1000000 INFO @ Sat, 08 Aug 2020 12:56:00: 5000000 INFO @ Sat, 08 Aug 2020 12:56:05: 2000000 INFO @ Sat, 08 Aug 2020 12:56:10: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sat, 08 Aug 2020 12:56:14: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:14: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:15: 3000000 INFO @ Sat, 08 Aug 2020 12:56:20: 7000000 INFO @ Sat, 08 Aug 2020 12:56:25: 1000000 INFO @ Sat, 08 Aug 2020 12:56:25: 4000000 INFO @ Sat, 08 Aug 2020 12:56:30: 8000000 INFO @ Sat, 08 Aug 2020 12:56:35: 2000000 INFO @ Sat, 08 Aug 2020 12:56:36: 5000000 INFO @ Sat, 08 Aug 2020 12:56:40: 9000000 INFO @ Sat, 08 Aug 2020 12:56:45: 3000000 INFO @ Sat, 08 Aug 2020 12:56:46: 6000000 INFO @ Sat, 08 Aug 2020 12:56:51: 10000000 INFO @ Sat, 08 Aug 2020 12:56:56: 4000000 INFO @ Sat, 08 Aug 2020 12:56:57: 7000000 INFO @ Sat, 08 Aug 2020 12:57:01: 11000000 INFO @ Sat, 08 Aug 2020 12:57:06: 5000000 INFO @ Sat, 08 Aug 2020 12:57:07: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:07: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:07: #1 total tags in treatment: 5236573 INFO @ Sat, 08 Aug 2020 12:57:07: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:57:07: #1 tags after filtering in treatment: 4892133 INFO @ Sat, 08 Aug 2020 12:57:07: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:57:07: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:07: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:07: 8000000 INFO @ Sat, 08 Aug 2020 12:57:07: #2 number of paired peaks: 466 WARNING @ Sat, 08 Aug 2020 12:57:07: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Sat, 08 Aug 2020 12:57:07: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:07: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:07: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:07: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:07: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 12:57:07: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 12:57:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.05_model.r WARNING @ Sat, 08 Aug 2020 12:57:07: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:57:07: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 12:57:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:57:07: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:57:17: 6000000 INFO @ Sat, 08 Aug 2020 12:57:17: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:57:19: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.05_summits.bed INFO @ Sat, 08 Aug 2020 12:57:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (406 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:57:27: 7000000 INFO @ Sat, 08 Aug 2020 12:57:28: 10000000 INFO @ Sat, 08 Aug 2020 12:57:37: 8000000 INFO @ Sat, 08 Aug 2020 12:57:38: 11000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:57:44: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:44: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:44: #1 total tags in treatment: 5236573 INFO @ Sat, 08 Aug 2020 12:57:44: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:57:44: #1 tags after filtering in treatment: 4892133 INFO @ Sat, 08 Aug 2020 12:57:44: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:57:44: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:44: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:44: #2 number of paired peaks: 466 WARNING @ Sat, 08 Aug 2020 12:57:44: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Sat, 08 Aug 2020 12:57:44: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:44: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:44: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:44: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:44: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 12:57:44: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 12:57:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.10_model.r WARNING @ Sat, 08 Aug 2020 12:57:44: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:57:44: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 12:57:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:57:44: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:57:47: 9000000 INFO @ Sat, 08 Aug 2020 12:57:55: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:57: 10000000 INFO @ Sat, 08 Aug 2020 12:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (273 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:06: 11000000 INFO @ Sat, 08 Aug 2020 12:58:12: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:12: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:12: #1 total tags in treatment: 5236573 INFO @ Sat, 08 Aug 2020 12:58:12: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:12: #1 tags after filtering in treatment: 4892133 INFO @ Sat, 08 Aug 2020 12:58:12: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:58:12: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:12: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:12: #2 number of paired peaks: 466 WARNING @ Sat, 08 Aug 2020 12:58:12: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:12: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:12: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:12: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:12: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:12: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 12:58:12: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 12:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.20_model.r WARNING @ Sat, 08 Aug 2020 12:58:12: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:12: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 12:58:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:12: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:23: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217789/SRX7217789.20_summits.bed INFO @ Sat, 08 Aug 2020 12:58:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling