Job ID = 6365892 SRX = SRX012300 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:20:14 prefetch.2.10.7: 1) Downloading 'SRR029219'... 2020-06-15T22:20:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:26:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:26:45 prefetch.2.10.7: 1) 'SRR029219' was downloaded successfully Read 13402463 spots for SRR029219/SRR029219.sra Written 13402463 spots for SRR029219/SRR029219.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:59 13402463 reads; of these: 13402463 (100.00%) were unpaired; of these: 5030037 (37.53%) aligned 0 times 6644177 (49.57%) aligned exactly 1 time 1728249 (12.90%) aligned >1 times 62.47% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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_rmdupse_core] 1470272 / 8372426 = 0.1756 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 07:31:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.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 07:31:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:57: 1000000 INFO @ Tue, 16 Jun 2020 07:32:03: 2000000 INFO @ Tue, 16 Jun 2020 07:32:09: 3000000 INFO @ Tue, 16 Jun 2020 07:32:16: 4000000 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 07:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.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 07:32:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:22: 5000000 INFO @ Tue, 16 Jun 2020 07:32:27: 1000000 INFO @ Tue, 16 Jun 2020 07:32:28: 6000000 INFO @ Tue, 16 Jun 2020 07:32:33: 2000000 INFO @ Tue, 16 Jun 2020 07:32:34: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:32:34: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:32:34: #1 total tags in treatment: 6902154 INFO @ Tue, 16 Jun 2020 07:32:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:34: #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 07:32:34: #1 tags after filtering in treatment: 6902154 INFO @ Tue, 16 Jun 2020 07:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:34: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:35: #2 number of paired peaks: 323 WARNING @ Tue, 16 Jun 2020 07:32:35: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Tue, 16 Jun 2020 07:32:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:35: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:32:35: #2 alternative fragment length(s) may be 1,34,81,484,512,521,527,551,589 bps INFO @ Tue, 16 Jun 2020 07:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.05_model.r WARNING @ Tue, 16 Jun 2020 07:32:35: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:32:35: #2 You may need to consider one of the other alternative d(s): 1,34,81,484,512,521,527,551,589 WARNING @ Tue, 16 Jun 2020 07:32:35: #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 07:32:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:39: 3000000 INFO @ Tue, 16 Jun 2020 07:32:44: 4000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 07:32:49: #3 Call peaks for each chromosome... 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 07:32:50: 5000000 INFO @ Tue, 16 Jun 2020 07:32:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.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 07:32:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:56: 6000000 INFO @ Tue, 16 Jun 2020 07:32:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.05_summits.bed INFO @ Tue, 16 Jun 2020 07:32:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:32:58: 1000000 INFO @ Tue, 16 Jun 2020 07:33:01: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:33:01: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:33:01: #1 total tags in treatment: 6902154 INFO @ Tue, 16 Jun 2020 07:33:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:01: #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 07:33:01: #1 tags after filtering in treatment: 6902154 INFO @ Tue, 16 Jun 2020 07:33:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:02: #2 number of paired peaks: 323 WARNING @ Tue, 16 Jun 2020 07:33:02: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Tue, 16 Jun 2020 07:33:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:02: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:33:02: #2 alternative fragment length(s) may be 1,34,81,484,512,521,527,551,589 bps INFO @ Tue, 16 Jun 2020 07:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.10_model.r WARNING @ Tue, 16 Jun 2020 07:33:02: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:33:02: #2 You may need to consider one of the other alternative d(s): 1,34,81,484,512,521,527,551,589 WARNING @ Tue, 16 Jun 2020 07:33:02: #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 07:33:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:33:04: 2000000 INFO @ Tue, 16 Jun 2020 07:33:10: 3000000 INFO @ Tue, 16 Jun 2020 07:33:16: 4000000 INFO @ Tue, 16 Jun 2020 07:33:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:23: 5000000 INFO @ Tue, 16 Jun 2020 07:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.10_summits.bed INFO @ Tue, 16 Jun 2020 07:33:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (67 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:33:29: 6000000 INFO @ Tue, 16 Jun 2020 07:33:35: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:33:35: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:33:35: #1 total tags in treatment: 6902154 INFO @ Tue, 16 Jun 2020 07:33:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:35: #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 07:33:35: #1 tags after filtering in treatment: 6902154 INFO @ Tue, 16 Jun 2020 07:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:36: #2 number of paired peaks: 323 WARNING @ Tue, 16 Jun 2020 07:33:36: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Tue, 16 Jun 2020 07:33:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:36: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:33:36: #2 alternative fragment length(s) may be 1,34,81,484,512,521,527,551,589 bps INFO @ Tue, 16 Jun 2020 07:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.20_model.r WARNING @ Tue, 16 Jun 2020 07:33:36: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:33:36: #2 You may need to consider one of the other alternative d(s): 1,34,81,484,512,521,527,551,589 WARNING @ Tue, 16 Jun 2020 07:33:36: #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 07:33:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:33:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012300/SRX012300.20_summits.bed INFO @ Tue, 16 Jun 2020 07:33:58: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling