Job ID = 6366958 SRX = SRX2576658 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:38 prefetch.2.10.7: 1) Downloading 'SRR5272615'... 2020-06-15T23:05:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:38 prefetch.2.10.7: 'SRR5272615' is valid 2020-06-15T23:06:38 prefetch.2.10.7: 1) 'SRR5272615' was downloaded successfully Read 19530987 spots for SRR5272615/SRR5272615.sra Written 19530987 spots for SRR5272615/SRR5272615.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:12 19530987 reads; of these: 19530987 (100.00%) were unpaired; of these: 136408 (0.70%) aligned 0 times 16098704 (82.43%) aligned exactly 1 time 3295875 (16.88%) aligned >1 times 99.30% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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 8 files... [bam_rmdupse_core] 2125818 / 19394579 = 0.1096 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 @ Tue, 16 Jun 2020 08:15:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.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 @ Tue, 16 Jun 2020 08:15:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:11: 1000000 INFO @ Tue, 16 Jun 2020 08:15:16: 2000000 INFO @ Tue, 16 Jun 2020 08:15:21: 3000000 INFO @ Tue, 16 Jun 2020 08:15:26: 4000000 INFO @ Tue, 16 Jun 2020 08:15:31: 5000000 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 @ Tue, 16 Jun 2020 08:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.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 @ Tue, 16 Jun 2020 08:15:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:36: 6000000 INFO @ Tue, 16 Jun 2020 08:15:41: 1000000 INFO @ Tue, 16 Jun 2020 08:15:41: 7000000 INFO @ Tue, 16 Jun 2020 08:15:47: 2000000 INFO @ Tue, 16 Jun 2020 08:15:47: 8000000 INFO @ Tue, 16 Jun 2020 08:15:52: 3000000 INFO @ Tue, 16 Jun 2020 08:15:52: 9000000 INFO @ Tue, 16 Jun 2020 08:15:57: 4000000 INFO @ Tue, 16 Jun 2020 08:15:58: 10000000 INFO @ Tue, 16 Jun 2020 08:16:02: 5000000 INFO @ Tue, 16 Jun 2020 08:16:03: 11000000 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 @ Tue, 16 Jun 2020 08:16:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.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 @ Tue, 16 Jun 2020 08:16:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:08: 6000000 INFO @ Tue, 16 Jun 2020 08:16:08: 12000000 INFO @ Tue, 16 Jun 2020 08:16:12: 1000000 INFO @ Tue, 16 Jun 2020 08:16:14: 7000000 INFO @ Tue, 16 Jun 2020 08:16:14: 13000000 INFO @ Tue, 16 Jun 2020 08:16:17: 2000000 INFO @ Tue, 16 Jun 2020 08:16:19: 14000000 INFO @ Tue, 16 Jun 2020 08:16:19: 8000000 INFO @ Tue, 16 Jun 2020 08:16:23: 3000000 INFO @ Tue, 16 Jun 2020 08:16:24: 15000000 INFO @ Tue, 16 Jun 2020 08:16:25: 9000000 INFO @ Tue, 16 Jun 2020 08:16:29: 4000000 INFO @ Tue, 16 Jun 2020 08:16:30: 16000000 INFO @ Tue, 16 Jun 2020 08:16:30: 10000000 INFO @ Tue, 16 Jun 2020 08:16:34: 5000000 INFO @ Tue, 16 Jun 2020 08:16:35: 17000000 INFO @ Tue, 16 Jun 2020 08:16:36: 11000000 INFO @ Tue, 16 Jun 2020 08:16:37: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:16:37: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:16:37: #1 total tags in treatment: 17268761 INFO @ Tue, 16 Jun 2020 08:16:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:16:37: #1 tags after filtering in treatment: 17268761 INFO @ Tue, 16 Jun 2020 08:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:38: #2 number of paired peaks: 227 WARNING @ Tue, 16 Jun 2020 08:16:38: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:38: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:16:38: #2 alternative fragment length(s) may be 1,33,525,574 bps INFO @ Tue, 16 Jun 2020 08:16:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.05_model.r WARNING @ Tue, 16 Jun 2020 08:16:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:38: #2 You may need to consider one of the other alternative d(s): 1,33,525,574 WARNING @ Tue, 16 Jun 2020 08:16:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:16:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:40: 6000000 INFO @ Tue, 16 Jun 2020 08:16:42: 12000000 INFO @ Tue, 16 Jun 2020 08:16:45: 7000000 INFO @ Tue, 16 Jun 2020 08:16:47: 13000000 INFO @ Tue, 16 Jun 2020 08:16:51: 8000000 INFO @ Tue, 16 Jun 2020 08:16:52: 14000000 INFO @ Tue, 16 Jun 2020 08:16:56: 9000000 INFO @ Tue, 16 Jun 2020 08:16:58: 15000000 INFO @ Tue, 16 Jun 2020 08:17:02: 10000000 INFO @ Tue, 16 Jun 2020 08:17:03: 16000000 INFO @ Tue, 16 Jun 2020 08:17:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:07: 11000000 INFO @ Tue, 16 Jun 2020 08:17:09: 17000000 INFO @ Tue, 16 Jun 2020 08:17:10: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:17:10: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:17:10: #1 total tags in treatment: 17268761 INFO @ Tue, 16 Jun 2020 08:17:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:17:10: #1 tags after filtering in treatment: 17268761 INFO @ Tue, 16 Jun 2020 08:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:12: #2 number of paired peaks: 227 WARNING @ Tue, 16 Jun 2020 08:17:12: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:12: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:17:12: #2 alternative fragment length(s) may be 1,33,525,574 bps INFO @ Tue, 16 Jun 2020 08:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.10_model.r WARNING @ Tue, 16 Jun 2020 08:17:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:12: #2 You may need to consider one of the other alternative d(s): 1,33,525,574 WARNING @ Tue, 16 Jun 2020 08:17:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:17:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:12: 12000000 INFO @ Tue, 16 Jun 2020 08:17:17: 13000000 INFO @ Tue, 16 Jun 2020 08:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.05_summits.bed INFO @ Tue, 16 Jun 2020 08:17:21: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:22: 14000000 INFO @ Tue, 16 Jun 2020 08:17:27: 15000000 INFO @ Tue, 16 Jun 2020 08:17:32: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:37: 17000000 INFO @ Tue, 16 Jun 2020 08:17:39: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:17:39: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:17:39: #1 total tags in treatment: 17268761 INFO @ Tue, 16 Jun 2020 08:17:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:17:39: #1 tags after filtering in treatment: 17268761 INFO @ Tue, 16 Jun 2020 08:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:40: #2 number of paired peaks: 227 WARNING @ Tue, 16 Jun 2020 08:17:40: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:17:40: #2 alternative fragment length(s) may be 1,33,525,574 bps INFO @ Tue, 16 Jun 2020 08:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.20_model.r WARNING @ Tue, 16 Jun 2020 08:17:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:40: #2 You may need to consider one of the other alternative d(s): 1,33,525,574 WARNING @ Tue, 16 Jun 2020 08:17:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:17:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.10_summits.bed INFO @ Tue, 16 Jun 2020 08:17:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576658/SRX2576658.20_summits.bed INFO @ Tue, 16 Jun 2020 08:18:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling