Job ID = 6368386 SRX = SRX495065 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:35 prefetch.2.10.7: 1) Downloading 'SRR1198597'... 2020-06-16T00:13:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:44 prefetch.2.10.7: 1) 'SRR1198597' was downloaded successfully Read 16047878 spots for SRR1198597/SRR1198597.sra Written 16047878 spots for SRR1198597/SRR1198597.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: 00:02:55 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1451127 (9.04%) aligned 0 times 12366184 (77.06%) aligned exactly 1 time 2230567 (13.90%) aligned >1 times 90.96% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 1645770 / 14596751 = 0.1127 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 09:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.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 09:25:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:13: 1000000 INFO @ Tue, 16 Jun 2020 09:25:20: 2000000 INFO @ Tue, 16 Jun 2020 09:25:27: 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 09:25:34: 4000000 INFO @ Tue, 16 Jun 2020 09:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.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 09:25:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:40: 5000000 INFO @ Tue, 16 Jun 2020 09:25:44: 1000000 INFO @ Tue, 16 Jun 2020 09:25:47: 6000000 INFO @ Tue, 16 Jun 2020 09:25:50: 2000000 INFO @ Tue, 16 Jun 2020 09:25:53: 7000000 INFO @ Tue, 16 Jun 2020 09:25:57: 3000000 INFO @ Tue, 16 Jun 2020 09:26:00: 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 09:26:05: 4000000 INFO @ Tue, 16 Jun 2020 09:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.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 09:26:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:07: 9000000 INFO @ Tue, 16 Jun 2020 09:26:12: 5000000 INFO @ Tue, 16 Jun 2020 09:26:13: 1000000 INFO @ Tue, 16 Jun 2020 09:26:14: 10000000 INFO @ Tue, 16 Jun 2020 09:26:19: 6000000 INFO @ Tue, 16 Jun 2020 09:26:21: 2000000 INFO @ Tue, 16 Jun 2020 09:26:22: 11000000 INFO @ Tue, 16 Jun 2020 09:26:26: 7000000 INFO @ Tue, 16 Jun 2020 09:26:29: 3000000 INFO @ Tue, 16 Jun 2020 09:26:30: 12000000 INFO @ Tue, 16 Jun 2020 09:26:33: 8000000 INFO @ Tue, 16 Jun 2020 09:26:36: 4000000 INFO @ Tue, 16 Jun 2020 09:26:36: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:36: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:36: #1 total tags in treatment: 12950981 INFO @ Tue, 16 Jun 2020 09:26:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:36: #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 09:26:37: #1 tags after filtering in treatment: 12950981 INFO @ Tue, 16 Jun 2020 09:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:38: #2 number of paired peaks: 280 WARNING @ Tue, 16 Jun 2020 09:26:38: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:38: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:26:38: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:26:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.05_model.r WARNING @ Tue, 16 Jun 2020 09:26:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:38: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:26:38: #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 09:26:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:41: 9000000 INFO @ Tue, 16 Jun 2020 09:26:43: 5000000 INFO @ Tue, 16 Jun 2020 09:26:48: 10000000 INFO @ Tue, 16 Jun 2020 09:26:51: 6000000 INFO @ Tue, 16 Jun 2020 09:26:55: 11000000 INFO @ Tue, 16 Jun 2020 09:26:59: 7000000 INFO @ Tue, 16 Jun 2020 09:27:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:02: 12000000 INFO @ Tue, 16 Jun 2020 09:27:06: 8000000 INFO @ Tue, 16 Jun 2020 09:27:09: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:27:09: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:27:09: #1 total tags in treatment: 12950981 INFO @ Tue, 16 Jun 2020 09:27:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:09: #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 09:27:09: #1 tags after filtering in treatment: 12950981 INFO @ Tue, 16 Jun 2020 09:27:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:10: #2 number of paired peaks: 280 WARNING @ Tue, 16 Jun 2020 09:27:10: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:10: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:27:10: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:27:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.10_model.r WARNING @ Tue, 16 Jun 2020 09:27:10: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:10: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:27:10: #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 09:27:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.05_summits.bed INFO @ Tue, 16 Jun 2020 09:27:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:14: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:27:22: 10000000 INFO @ Tue, 16 Jun 2020 09:27:31: 11000000 INFO @ Tue, 16 Jun 2020 09:27:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:39: 12000000 INFO @ Tue, 16 Jun 2020 09:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (362 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:46: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:27:46: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:27:46: #1 total tags in treatment: 12950981 INFO @ Tue, 16 Jun 2020 09:27:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:46: #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 09:27:47: #1 tags after filtering in treatment: 12950981 INFO @ Tue, 16 Jun 2020 09:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:47: #2 number of paired peaks: 280 WARNING @ Tue, 16 Jun 2020 09:27:47: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:48: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:27:48: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.20_model.r WARNING @ Tue, 16 Jun 2020 09:27:48: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:48: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:27:48: #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 09:27:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:28:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495065/SRX495065.20_summits.bed INFO @ Tue, 16 Jun 2020 09:28:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling