Job ID = 6368717 SRX = SRX5402741 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:04 prefetch.2.10.7: 1) Downloading 'SRR8602975'... 2020-06-16T00:27:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:50 prefetch.2.10.7: 1) 'SRR8602975' was downloaded successfully Read 32344770 spots for SRR8602975/SRR8602975.sra Written 32344770 spots for SRR8602975/SRR8602975.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: 00:06:43 32344770 reads; of these: 32344770 (100.00%) were unpaired; of these: 9517408 (29.42%) aligned 0 times 14598945 (45.14%) aligned exactly 1 time 8228417 (25.44%) aligned >1 times 70.58% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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 12 files... [bam_rmdupse_core] 7530142 / 22827362 = 0.3299 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 09:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.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 09:47:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:35: 1000000 INFO @ Tue, 16 Jun 2020 09:47:42: 2000000 INFO @ Tue, 16 Jun 2020 09:47:48: 3000000 INFO @ Tue, 16 Jun 2020 09:47:54: 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 09:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.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 09:47:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:00: 5000000 INFO @ Tue, 16 Jun 2020 09:48:06: 1000000 INFO @ Tue, 16 Jun 2020 09:48:06: 6000000 INFO @ Tue, 16 Jun 2020 09:48:12: 2000000 INFO @ Tue, 16 Jun 2020 09:48:12: 7000000 INFO @ Tue, 16 Jun 2020 09:48:18: 8000000 INFO @ Tue, 16 Jun 2020 09:48:18: 3000000 INFO @ Tue, 16 Jun 2020 09:48:24: 9000000 INFO @ Tue, 16 Jun 2020 09:48:24: 4000000 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 09:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.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 09:48:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:31: 10000000 INFO @ Tue, 16 Jun 2020 09:48:31: 5000000 INFO @ Tue, 16 Jun 2020 09:48:36: 1000000 INFO @ Tue, 16 Jun 2020 09:48:38: 11000000 INFO @ Tue, 16 Jun 2020 09:48:39: 6000000 INFO @ Tue, 16 Jun 2020 09:48:43: 2000000 INFO @ Tue, 16 Jun 2020 09:48:45: 12000000 INFO @ Tue, 16 Jun 2020 09:48:46: 7000000 INFO @ Tue, 16 Jun 2020 09:48:50: 3000000 INFO @ Tue, 16 Jun 2020 09:48:52: 13000000 INFO @ Tue, 16 Jun 2020 09:48:53: 8000000 INFO @ Tue, 16 Jun 2020 09:48:57: 4000000 INFO @ Tue, 16 Jun 2020 09:48:58: 14000000 INFO @ Tue, 16 Jun 2020 09:49:00: 9000000 INFO @ Tue, 16 Jun 2020 09:49:03: 5000000 INFO @ Tue, 16 Jun 2020 09:49:05: 15000000 INFO @ Tue, 16 Jun 2020 09:49:07: 10000000 INFO @ Tue, 16 Jun 2020 09:49:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:07: #1 total tags in treatment: 15297220 INFO @ Tue, 16 Jun 2020 09:49:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:07: #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 09:49:07: #1 tags after filtering in treatment: 15297220 INFO @ Tue, 16 Jun 2020 09:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:09: #2 number of paired peaks: 1283 INFO @ Tue, 16 Jun 2020 09:49:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:09: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:49:09: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 09:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:09: #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 09:49:09: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 09:49:09: #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 09:49:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:09: 6000000 INFO @ Tue, 16 Jun 2020 09:49:14: 11000000 INFO @ Tue, 16 Jun 2020 09:49:15: 7000000 INFO @ Tue, 16 Jun 2020 09:49:20: 12000000 INFO @ Tue, 16 Jun 2020 09:49:22: 8000000 INFO @ Tue, 16 Jun 2020 09:49:27: 13000000 INFO @ Tue, 16 Jun 2020 09:49:28: 9000000 INFO @ Tue, 16 Jun 2020 09:49:33: 14000000 INFO @ Tue, 16 Jun 2020 09:49:34: 10000000 INFO @ Tue, 16 Jun 2020 09:49:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:40: 15000000 INFO @ Tue, 16 Jun 2020 09:49:41: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:49:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:42: #1 total tags in treatment: 15297220 INFO @ Tue, 16 Jun 2020 09:49:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:42: #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 09:49:42: #1 tags after filtering in treatment: 15297220 INFO @ Tue, 16 Jun 2020 09:49:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:44: #2 number of paired peaks: 1283 INFO @ Tue, 16 Jun 2020 09:49:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:44: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:49:44: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 09:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:44: #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 09:49:44: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 09:49:44: #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 09:49:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:47: 12000000 INFO @ Tue, 16 Jun 2020 09:49:54: 13000000 INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8491 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:00: 14000000 INFO @ Tue, 16 Jun 2020 09:50:06: 15000000 INFO @ Tue, 16 Jun 2020 09:50:08: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:08: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:08: #1 total tags in treatment: 15297220 INFO @ Tue, 16 Jun 2020 09:50:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:08: #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 09:50:08: #1 tags after filtering in treatment: 15297220 INFO @ Tue, 16 Jun 2020 09:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:09: #2 number of paired peaks: 1283 INFO @ Tue, 16 Jun 2020 09:50:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:09: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:50:09: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 09:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:09: #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 09:50:09: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 09:50:09: #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 09:50:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3758 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402741/SRX5402741.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (949 records, 4 fields): 3 millis CompletedMACS2peakCalling