Job ID = 6366856 SRX = SRX2350755 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:23 prefetch.2.10.7: 1) Downloading 'SRR5024064'... 2020-06-15T23:06:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:56 prefetch.2.10.7: 'SRR5024064' is valid 2020-06-15T23:07:56 prefetch.2.10.7: 1) 'SRR5024064' was downloaded successfully Read 11427736 spots for SRR5024064/SRR5024064.sra Written 11427736 spots for SRR5024064/SRR5024064.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: 00:02:29 11427736 reads; of these: 11427736 (100.00%) were unpaired; of these: 473420 (4.14%) aligned 0 times 9642418 (84.38%) aligned exactly 1 time 1311898 (11.48%) aligned >1 times 95.86% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 1521696 / 10954316 = 0.1389 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 08:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.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 08:14:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:15: 1000000 INFO @ Tue, 16 Jun 2020 08:14:22: 2000000 INFO @ Tue, 16 Jun 2020 08:14:29: 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 @ Tue, 16 Jun 2020 08:14:36: 4000000 INFO @ Tue, 16 Jun 2020 08:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.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 08:14:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:44: 5000000 INFO @ Tue, 16 Jun 2020 08:14:45: 1000000 INFO @ Tue, 16 Jun 2020 08:14:51: 6000000 INFO @ Tue, 16 Jun 2020 08:14:51: 2000000 INFO @ Tue, 16 Jun 2020 08:14:57: 3000000 INFO @ Tue, 16 Jun 2020 08:14:58: 7000000 INFO @ Tue, 16 Jun 2020 08:15:04: 4000000 INFO @ Tue, 16 Jun 2020 08:15:05: 8000000 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 08:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.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 08:15:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:10: 5000000 INFO @ Tue, 16 Jun 2020 08:15:12: 9000000 INFO @ Tue, 16 Jun 2020 08:15:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:15: #1 total tags in treatment: 9432620 INFO @ Tue, 16 Jun 2020 08:15:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:15: #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 08:15:15: #1 tags after filtering in treatment: 9432620 INFO @ Tue, 16 Jun 2020 08:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:15: 1000000 INFO @ Tue, 16 Jun 2020 08:15:16: #2 number of paired peaks: 242 WARNING @ Tue, 16 Jun 2020 08:15:16: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:16: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:15:16: #2 alternative fragment length(s) may be 3,50,125,170,197,439,455,588 bps INFO @ Tue, 16 Jun 2020 08:15:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.05_model.r WARNING @ Tue, 16 Jun 2020 08:15:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:16: #2 You may need to consider one of the other alternative d(s): 3,50,125,170,197,439,455,588 WARNING @ Tue, 16 Jun 2020 08:15:16: #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 08:15:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:16: 6000000 INFO @ Tue, 16 Jun 2020 08:15:23: 2000000 INFO @ Tue, 16 Jun 2020 08:15:23: 7000000 INFO @ Tue, 16 Jun 2020 08:15:29: 8000000 INFO @ Tue, 16 Jun 2020 08:15:30: 3000000 INFO @ Tue, 16 Jun 2020 08:15:35: 9000000 INFO @ Tue, 16 Jun 2020 08:15:37: 4000000 INFO @ Tue, 16 Jun 2020 08:15:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:38: #1 total tags in treatment: 9432620 INFO @ Tue, 16 Jun 2020 08:15:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:38: #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 08:15:38: #1 tags after filtering in treatment: 9432620 INFO @ Tue, 16 Jun 2020 08:15:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:39: #2 number of paired peaks: 242 WARNING @ Tue, 16 Jun 2020 08:15:39: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:39: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:15:39: #2 alternative fragment length(s) may be 3,50,125,170,197,439,455,588 bps INFO @ Tue, 16 Jun 2020 08:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:39: #2 You may need to consider one of the other alternative d(s): 3,50,125,170,197,439,455,588 WARNING @ Tue, 16 Jun 2020 08:15:39: #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 08:15:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:43: 5000000 INFO @ Tue, 16 Jun 2020 08:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:50: 6000000 INFO @ Tue, 16 Jun 2020 08:15:56: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:03: 8000000 INFO @ Tue, 16 Jun 2020 08:16:10: 9000000 INFO @ Tue, 16 Jun 2020 08:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:16:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:16:12: #1 total tags in treatment: 9432620 INFO @ Tue, 16 Jun 2020 08:16:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:12: #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 08:16:13: #1 tags after filtering in treatment: 9432620 INFO @ Tue, 16 Jun 2020 08:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:13: #2 number of paired peaks: 242 WARNING @ Tue, 16 Jun 2020 08:16:13: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:13: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:16:13: #2 alternative fragment length(s) may be 3,50,125,170,197,439,455,588 bps INFO @ Tue, 16 Jun 2020 08:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.20_model.r WARNING @ Tue, 16 Jun 2020 08:16:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:13: #2 You may need to consider one of the other alternative d(s): 3,50,125,170,197,439,455,588 WARNING @ Tue, 16 Jun 2020 08:16:13: #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 08:16:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350755/SRX2350755.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling