Job ID = 6368810 SRX = SRX5985664 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:16 prefetch.2.10.7: 1) Downloading 'SRR9214969'... 2020-06-16T00:30:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:34:04 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:34:04 prefetch.2.10.7: 1) 'SRR9214969' was downloaded successfully Read 17075468 spots for SRR9214969/SRR9214969.sra Written 17075468 spots for SRR9214969/SRR9214969.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: 00:05:19 17075468 reads; of these: 17075468 (100.00%) were unpaired; of these: 601737 (3.52%) aligned 0 times 14708689 (86.14%) aligned exactly 1 time 1765042 (10.34%) aligned >1 times 96.48% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 2644860 / 16473731 = 0.1606 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 09:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.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 09:46:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:44: 1000000 INFO @ Tue, 16 Jun 2020 09:46:51: 2000000 INFO @ Tue, 16 Jun 2020 09:46:58: 3000000 INFO @ Tue, 16 Jun 2020 09:47:04: 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 09:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.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 09:47:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:11: 5000000 INFO @ Tue, 16 Jun 2020 09:47:15: 1000000 INFO @ Tue, 16 Jun 2020 09:47:18: 6000000 INFO @ Tue, 16 Jun 2020 09:47:22: 2000000 INFO @ Tue, 16 Jun 2020 09:47:25: 7000000 INFO @ Tue, 16 Jun 2020 09:47:29: 3000000 INFO @ Tue, 16 Jun 2020 09:47:32: 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 09:47:36: 4000000 INFO @ Tue, 16 Jun 2020 09:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.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 09:47:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:39: 9000000 INFO @ Tue, 16 Jun 2020 09:47:43: 5000000 INFO @ Tue, 16 Jun 2020 09:47:45: 1000000 INFO @ Tue, 16 Jun 2020 09:47:47: 10000000 INFO @ Tue, 16 Jun 2020 09:47:51: 6000000 INFO @ Tue, 16 Jun 2020 09:47:53: 2000000 INFO @ Tue, 16 Jun 2020 09:47:54: 11000000 INFO @ Tue, 16 Jun 2020 09:47:58: 7000000 INFO @ Tue, 16 Jun 2020 09:48:01: 3000000 INFO @ Tue, 16 Jun 2020 09:48:02: 12000000 INFO @ Tue, 16 Jun 2020 09:48:06: 8000000 INFO @ Tue, 16 Jun 2020 09:48:08: 4000000 INFO @ Tue, 16 Jun 2020 09:48:10: 13000000 INFO @ Tue, 16 Jun 2020 09:48:13: 9000000 INFO @ Tue, 16 Jun 2020 09:48:15: 5000000 INFO @ Tue, 16 Jun 2020 09:48:16: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:48:16: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:48:16: #1 total tags in treatment: 13828871 INFO @ Tue, 16 Jun 2020 09:48:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:16: #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 09:48:16: #1 tags after filtering in treatment: 13828871 INFO @ Tue, 16 Jun 2020 09:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:17: #2 number of paired peaks: 1356 INFO @ Tue, 16 Jun 2020 09:48:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:17: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 09:48:17: #2 alternative fragment length(s) may be 4,123 bps INFO @ Tue, 16 Jun 2020 09:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:17: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:17: #2 You may need to consider one of the other alternative d(s): 4,123 WARNING @ Tue, 16 Jun 2020 09:48:17: #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 09:48:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:21: 10000000 INFO @ Tue, 16 Jun 2020 09:48:23: 6000000 INFO @ Tue, 16 Jun 2020 09:48:28: 11000000 INFO @ Tue, 16 Jun 2020 09:48:30: 7000000 INFO @ Tue, 16 Jun 2020 09:48:35: 12000000 INFO @ Tue, 16 Jun 2020 09:48:37: 8000000 INFO @ Tue, 16 Jun 2020 09:48:43: 13000000 INFO @ Tue, 16 Jun 2020 09:48:45: 9000000 INFO @ Tue, 16 Jun 2020 09:48:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:49: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:48:49: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:48:49: #1 total tags in treatment: 13828871 INFO @ Tue, 16 Jun 2020 09:48:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:49: #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 09:48:49: #1 tags after filtering in treatment: 13828871 INFO @ Tue, 16 Jun 2020 09:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:50: #2 number of paired peaks: 1356 INFO @ Tue, 16 Jun 2020 09:48:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:50: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 09:48:50: #2 alternative fragment length(s) may be 4,123 bps INFO @ Tue, 16 Jun 2020 09:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.10_model.r WARNING @ Tue, 16 Jun 2020 09:48:50: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:50: #2 You may need to consider one of the other alternative d(s): 4,123 WARNING @ Tue, 16 Jun 2020 09:48:50: #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 09:48:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:52: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:59: 11000000 INFO @ Tue, 16 Jun 2020 09:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5642 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:06: 12000000 INFO @ Tue, 16 Jun 2020 09:49:13: 13000000 INFO @ Tue, 16 Jun 2020 09:49:19: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:49:19: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:49:19: #1 total tags in treatment: 13828871 INFO @ Tue, 16 Jun 2020 09:49:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:19: #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 09:49:19: #1 tags after filtering in treatment: 13828871 INFO @ Tue, 16 Jun 2020 09:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:20: #2 number of paired peaks: 1356 INFO @ Tue, 16 Jun 2020 09:49:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:20: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 09:49:20: #2 alternative fragment length(s) may be 4,123 bps INFO @ Tue, 16 Jun 2020 09:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:20: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:20: #2 You may need to consider one of the other alternative d(s): 4,123 WARNING @ Tue, 16 Jun 2020 09:49:20: #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 09:49:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3197 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985664/SRX5985664.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1364 records, 4 fields): 3 millis CompletedMACS2peakCalling