Job ID = 6367727 SRX = SRX4082341 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:38:44 prefetch.2.10.7: 1) Downloading 'SRR7164159'... 2020-06-15T23:38:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:25 prefetch.2.10.7: 'SRR7164159' is valid 2020-06-15T23:41:25 prefetch.2.10.7: 1) 'SRR7164159' was downloaded successfully 2020-06-15T23:41:25 prefetch.2.10.7: 'SRR7164159' has 0 unresolved dependencies Read 15407052 spots for SRR7164159/SRR7164159.sra Written 15407052 spots for SRR7164159/SRR7164159.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: 00:02:56 15407052 reads; of these: 15407052 (100.00%) were unpaired; of these: 5232411 (33.96%) aligned 0 times 9215085 (59.81%) aligned exactly 1 time 959556 (6.23%) aligned >1 times 66.04% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 1677497 / 10174641 = 0.1649 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 08:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.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 08:48:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:05: 1000000 INFO @ Tue, 16 Jun 2020 08:49:13: 2000000 INFO @ Tue, 16 Jun 2020 08:49:21: 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 08:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.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 08:49:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:29: 4000000 INFO @ Tue, 16 Jun 2020 08:49:36: 1000000 INFO @ Tue, 16 Jun 2020 08:49:37: 5000000 INFO @ Tue, 16 Jun 2020 08:49:43: 2000000 INFO @ Tue, 16 Jun 2020 08:49:45: 6000000 INFO @ Tue, 16 Jun 2020 08:49:51: 3000000 INFO @ Tue, 16 Jun 2020 08:49:53: 7000000 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 08:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.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 08:49:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:59: 4000000 INFO @ Tue, 16 Jun 2020 08:50:01: 8000000 INFO @ Tue, 16 Jun 2020 08:50:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:05: #1 total tags in treatment: 8497144 INFO @ Tue, 16 Jun 2020 08:50:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:05: #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 08:50:05: #1 tags after filtering in treatment: 8497144 INFO @ Tue, 16 Jun 2020 08:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:06: 1000000 INFO @ Tue, 16 Jun 2020 08:50:06: #2 number of paired peaks: 5053 INFO @ Tue, 16 Jun 2020 08:50:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:07: 5000000 INFO @ Tue, 16 Jun 2020 08:50:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:07: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:50:07: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.05_model.r INFO @ Tue, 16 Jun 2020 08:50:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:14: 2000000 INFO @ Tue, 16 Jun 2020 08:50:15: 6000000 INFO @ Tue, 16 Jun 2020 08:50:22: 3000000 INFO @ Tue, 16 Jun 2020 08:50:23: 7000000 INFO @ Tue, 16 Jun 2020 08:50:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:30: 4000000 INFO @ Tue, 16 Jun 2020 08:50:31: 8000000 INFO @ Tue, 16 Jun 2020 08:50:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:34: #1 total tags in treatment: 8497144 INFO @ Tue, 16 Jun 2020 08:50:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:34: #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 08:50:35: #1 tags after filtering in treatment: 8497144 INFO @ Tue, 16 Jun 2020 08:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:36: #2 number of paired peaks: 5053 INFO @ Tue, 16 Jun 2020 08:50:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:36: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:50:36: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.10_model.r INFO @ Tue, 16 Jun 2020 08:50:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:38: 5000000 INFO @ Tue, 16 Jun 2020 08:50:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6652 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:46: 6000000 INFO @ Tue, 16 Jun 2020 08:50:55: 7000000 INFO @ Tue, 16 Jun 2020 08:50:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:03: 8000000 INFO @ Tue, 16 Jun 2020 08:51:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:07: #1 total tags in treatment: 8497144 INFO @ Tue, 16 Jun 2020 08:51:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:07: #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 08:51:07: #1 tags after filtering in treatment: 8497144 INFO @ Tue, 16 Jun 2020 08:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:08: #2 number of paired peaks: 5053 INFO @ Tue, 16 Jun 2020 08:51:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:08: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:51:08: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 16 Jun 2020 08:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.20_model.r INFO @ Tue, 16 Jun 2020 08:51:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5161 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082341/SRX4082341.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4001 records, 4 fields): 8 millis CompletedMACS2peakCalling