Job ID = 6367032 SRX = SRX2737091 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:16 prefetch.2.10.7: 1) Downloading 'SRR5448129'... 2020-06-15T23:18:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:19:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:19:56 prefetch.2.10.7: 1) 'SRR5448129' was downloaded successfully 2020-06-15T23:19:56 prefetch.2.10.7: 'SRR5448129' has 0 unresolved dependencies Read 33396816 spots for SRR5448129/SRR5448129.sra Written 33396816 spots for SRR5448129/SRR5448129.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: 00:07:06 33396816 reads; of these: 33396816 (100.00%) were unpaired; of these: 3287985 (9.85%) aligned 0 times 26193625 (78.43%) aligned exactly 1 time 3915206 (11.72%) aligned >1 times 90.15% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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] 10009351 / 30108831 = 0.3324 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 08:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.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 08:34:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:06: 1000000 INFO @ Tue, 16 Jun 2020 08:34:11: 2000000 INFO @ Tue, 16 Jun 2020 08:34:17: 3000000 INFO @ Tue, 16 Jun 2020 08:34:22: 4000000 INFO @ Tue, 16 Jun 2020 08:34:28: 5000000 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 08:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.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 08:34:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:34: 6000000 INFO @ Tue, 16 Jun 2020 08:34:37: 1000000 INFO @ Tue, 16 Jun 2020 08:34:40: 7000000 INFO @ Tue, 16 Jun 2020 08:34:44: 2000000 INFO @ Tue, 16 Jun 2020 08:34:47: 8000000 INFO @ Tue, 16 Jun 2020 08:34:50: 3000000 INFO @ Tue, 16 Jun 2020 08:34:53: 9000000 INFO @ Tue, 16 Jun 2020 08:34:56: 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 08:34:59: 10000000 INFO @ Tue, 16 Jun 2020 08:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.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 08:35:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:03: 5000000 INFO @ Tue, 16 Jun 2020 08:35:06: 11000000 INFO @ Tue, 16 Jun 2020 08:35:07: 1000000 INFO @ Tue, 16 Jun 2020 08:35:09: 6000000 INFO @ Tue, 16 Jun 2020 08:35:12: 12000000 INFO @ Tue, 16 Jun 2020 08:35:13: 2000000 INFO @ Tue, 16 Jun 2020 08:35:16: 7000000 INFO @ Tue, 16 Jun 2020 08:35:19: 13000000 INFO @ Tue, 16 Jun 2020 08:35:20: 3000000 INFO @ Tue, 16 Jun 2020 08:35:23: 8000000 INFO @ Tue, 16 Jun 2020 08:35:26: 14000000 INFO @ Tue, 16 Jun 2020 08:35:26: 4000000 INFO @ Tue, 16 Jun 2020 08:35:29: 9000000 INFO @ Tue, 16 Jun 2020 08:35:32: 15000000 INFO @ Tue, 16 Jun 2020 08:35:33: 5000000 INFO @ Tue, 16 Jun 2020 08:35:36: 10000000 INFO @ Tue, 16 Jun 2020 08:35:39: 16000000 INFO @ Tue, 16 Jun 2020 08:35:39: 6000000 INFO @ Tue, 16 Jun 2020 08:35:42: 11000000 INFO @ Tue, 16 Jun 2020 08:35:45: 17000000 INFO @ Tue, 16 Jun 2020 08:35:46: 7000000 INFO @ Tue, 16 Jun 2020 08:35:49: 12000000 INFO @ Tue, 16 Jun 2020 08:35:52: 18000000 INFO @ Tue, 16 Jun 2020 08:35:52: 8000000 INFO @ Tue, 16 Jun 2020 08:35:56: 13000000 INFO @ Tue, 16 Jun 2020 08:35:58: 19000000 INFO @ Tue, 16 Jun 2020 08:35:59: 9000000 INFO @ Tue, 16 Jun 2020 08:36:02: 14000000 INFO @ Tue, 16 Jun 2020 08:36:05: 20000000 INFO @ Tue, 16 Jun 2020 08:36:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:05: #1 total tags in treatment: 20099480 INFO @ Tue, 16 Jun 2020 08:36:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:05: #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 08:36:05: 10000000 INFO @ Tue, 16 Jun 2020 08:36:06: #1 tags after filtering in treatment: 20099480 INFO @ Tue, 16 Jun 2020 08:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:07: #2 number of paired peaks: 1902 INFO @ Tue, 16 Jun 2020 08:36:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:08: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:36:08: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 08:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.05_model.r INFO @ Tue, 16 Jun 2020 08:36:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:09: 15000000 INFO @ Tue, 16 Jun 2020 08:36:12: 11000000 INFO @ Tue, 16 Jun 2020 08:36:16: 16000000 INFO @ Tue, 16 Jun 2020 08:36:18: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:22: 17000000 INFO @ Tue, 16 Jun 2020 08:36:25: 13000000 INFO @ Tue, 16 Jun 2020 08:36:29: 18000000 INFO @ Tue, 16 Jun 2020 08:36:31: 14000000 INFO @ Tue, 16 Jun 2020 08:36:35: 19000000 INFO @ Tue, 16 Jun 2020 08:36:38: 15000000 INFO @ Tue, 16 Jun 2020 08:36:42: 20000000 INFO @ Tue, 16 Jun 2020 08:36:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:43: #1 total tags in treatment: 20099480 INFO @ Tue, 16 Jun 2020 08:36:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:43: #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 08:36:43: #1 tags after filtering in treatment: 20099480 INFO @ Tue, 16 Jun 2020 08:36:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:44: 16000000 INFO @ Tue, 16 Jun 2020 08:36:45: #2 number of paired peaks: 1902 INFO @ Tue, 16 Jun 2020 08:36:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:45: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:36:45: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 08:36:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.10_model.r INFO @ Tue, 16 Jun 2020 08:36:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:50: 17000000 INFO @ Tue, 16 Jun 2020 08:36:56: 18000000 INFO @ Tue, 16 Jun 2020 08:36:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:02: 19000000 INFO @ Tue, 16 Jun 2020 08:37:08: 20000000 INFO @ Tue, 16 Jun 2020 08:37:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:37:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:37:09: #1 total tags in treatment: 20099480 INFO @ Tue, 16 Jun 2020 08:37:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:09: #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 08:37:09: #1 tags after filtering in treatment: 20099480 INFO @ Tue, 16 Jun 2020 08:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:11: #2 number of paired peaks: 1902 INFO @ Tue, 16 Jun 2020 08:37:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:11: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:37:11: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 08:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.20_model.r INFO @ Tue, 16 Jun 2020 08:37:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8251 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5466 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737091/SRX2737091.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2833 records, 4 fields): 4 millis CompletedMACS2peakCalling