Job ID = 6366648 SRX = SRX2163949 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:53 prefetch.2.10.7: 1) Downloading 'SRR4242864'... 2020-06-15T23:01:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:56 prefetch.2.10.7: 1) 'SRR4242864' was downloaded successfully Read 41298351 spots for SRR4242864/SRR4242864.sra Written 41298351 spots for SRR4242864/SRR4242864.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: 00:14:02 41298351 reads; of these: 41298351 (100.00%) were unpaired; of these: 9783234 (23.69%) aligned 0 times 27298487 (66.10%) aligned exactly 1 time 4216630 (10.21%) aligned >1 times 76.31% overall alignment rate Time searching: 00:14:02 Overall time: 00:14:02 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 16 files... [bam_rmdupse_core] 14723555 / 31515117 = 0.4672 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 08:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.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 08:33:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:35: 1000000 INFO @ Tue, 16 Jun 2020 08:33:44: 2000000 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 08:33:53: 3000000 INFO @ Tue, 16 Jun 2020 08:33:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.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 08:33:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:03: 4000000 INFO @ Tue, 16 Jun 2020 08:34:04: 1000000 INFO @ Tue, 16 Jun 2020 08:34:13: 2000000 INFO @ Tue, 16 Jun 2020 08:34:14: 5000000 INFO @ Tue, 16 Jun 2020 08:34:22: 3000000 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 08:34:24: 6000000 INFO @ Tue, 16 Jun 2020 08:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.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 08:34:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:31: 4000000 INFO @ Tue, 16 Jun 2020 08:34:34: 1000000 INFO @ Tue, 16 Jun 2020 08:34:34: 7000000 INFO @ Tue, 16 Jun 2020 08:34:40: 5000000 INFO @ Tue, 16 Jun 2020 08:34:43: 2000000 INFO @ Tue, 16 Jun 2020 08:34:45: 8000000 INFO @ Tue, 16 Jun 2020 08:34:49: 6000000 INFO @ Tue, 16 Jun 2020 08:34:52: 3000000 INFO @ Tue, 16 Jun 2020 08:34:56: 9000000 INFO @ Tue, 16 Jun 2020 08:34:58: 7000000 INFO @ Tue, 16 Jun 2020 08:35:02: 4000000 INFO @ Tue, 16 Jun 2020 08:35:05: 10000000 INFO @ Tue, 16 Jun 2020 08:35:07: 8000000 INFO @ Tue, 16 Jun 2020 08:35:11: 5000000 INFO @ Tue, 16 Jun 2020 08:35:15: 11000000 INFO @ Tue, 16 Jun 2020 08:35:16: 9000000 INFO @ Tue, 16 Jun 2020 08:35:20: 6000000 INFO @ Tue, 16 Jun 2020 08:35:25: 10000000 INFO @ Tue, 16 Jun 2020 08:35:25: 12000000 INFO @ Tue, 16 Jun 2020 08:35:29: 7000000 INFO @ Tue, 16 Jun 2020 08:35:34: 11000000 INFO @ Tue, 16 Jun 2020 08:35:35: 13000000 INFO @ Tue, 16 Jun 2020 08:35:38: 8000000 INFO @ Tue, 16 Jun 2020 08:35:43: 12000000 INFO @ Tue, 16 Jun 2020 08:35:44: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:48: 9000000 INFO @ Tue, 16 Jun 2020 08:35:52: 13000000 INFO @ Tue, 16 Jun 2020 08:35:54: 15000000 INFO @ Tue, 16 Jun 2020 08:35:57: 10000000 INFO @ Tue, 16 Jun 2020 08:36:01: 14000000 INFO @ Tue, 16 Jun 2020 08:36:03: 16000000 INFO @ Tue, 16 Jun 2020 08:36:06: 11000000 INFO @ Tue, 16 Jun 2020 08:36:10: 15000000 INFO @ Tue, 16 Jun 2020 08:36:11: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:36:11: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:36:11: #1 total tags in treatment: 16791562 INFO @ Tue, 16 Jun 2020 08:36:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:11: #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 08:36:12: #1 tags after filtering in treatment: 16791562 INFO @ Tue, 16 Jun 2020 08:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:13: #2 number of paired peaks: 1397 INFO @ Tue, 16 Jun 2020 08:36:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:13: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:36:13: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 16 Jun 2020 08:36:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.05_model.r WARNING @ Tue, 16 Jun 2020 08:36:13: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:13: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 16 Jun 2020 08:36:13: #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 08:36:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:14: 12000000 INFO @ Tue, 16 Jun 2020 08:36:18: 16000000 INFO @ Tue, 16 Jun 2020 08:36:23: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:25: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:36:25: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:36:25: #1 total tags in treatment: 16791562 INFO @ Tue, 16 Jun 2020 08:36:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:25: #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 08:36:25: #1 tags after filtering in treatment: 16791562 INFO @ Tue, 16 Jun 2020 08:36:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:26: #2 number of paired peaks: 1397 INFO @ Tue, 16 Jun 2020 08:36:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:26: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:36:26: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 16 Jun 2020 08:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:26: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:26: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 16 Jun 2020 08:36:26: #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 08:36:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:30: 14000000 INFO @ Tue, 16 Jun 2020 08:36:38: 15000000 INFO @ Tue, 16 Jun 2020 08:36:45: 16000000 INFO @ Tue, 16 Jun 2020 08:36:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:51: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:36:51: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:36:51: #1 total tags in treatment: 16791562 INFO @ Tue, 16 Jun 2020 08:36:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:51: #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 08:36:52: #1 tags after filtering in treatment: 16791562 INFO @ Tue, 16 Jun 2020 08:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:53: #2 number of paired peaks: 1397 INFO @ Tue, 16 Jun 2020 08:36:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:53: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:36:53: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 16 Jun 2020 08:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.20_model.r WARNING @ Tue, 16 Jun 2020 08:36:53: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:53: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 16 Jun 2020 08:36:53: #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 08:36:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5071 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3904 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163949/SRX2163949.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2839 records, 4 fields): 4 millis CompletedMACS2peakCalling