Job ID = 6365983 SRX = SRX043994 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:20:59 prefetch.2.10.7: 1) Downloading 'SRR107572'... 2020-06-15T22:20:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:21:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:21:34 prefetch.2.10.7: 'SRR107572' is valid 2020-06-15T22:21:34 prefetch.2.10.7: 1) 'SRR107572' was downloaded successfully Read 4526980 spots for SRR107572/SRR107572.sra Written 4526980 spots for SRR107572/SRR107572.sra 2020-06-15T22:21:59 prefetch.2.10.7: 1) Downloading 'SRR107573'... 2020-06-15T22:21:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:22:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:22:27 prefetch.2.10.7: 'SRR107573' is valid 2020-06-15T22:22:27 prefetch.2.10.7: 1) 'SRR107573' was downloaded successfully Read 4622207 spots for SRR107573/SRR107573.sra Written 4622207 spots for SRR107573/SRR107573.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: 00:01:25 9149187 reads; of these: 9149187 (100.00%) were unpaired; of these: 759451 (8.30%) aligned 0 times 7524485 (82.24%) aligned exactly 1 time 865251 (9.46%) aligned >1 times 91.70% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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_rmdupse_core] 1648127 / 8389736 = 0.1964 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 07:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.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 07:26:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:26:44: 1000000 INFO @ Tue, 16 Jun 2020 07:26:50: 2000000 INFO @ Tue, 16 Jun 2020 07:26:56: 3000000 INFO @ Tue, 16 Jun 2020 07:27:02: 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 07:27:08: 5000000 INFO @ Tue, 16 Jun 2020 07:27:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.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 07:27:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:27:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:14: 6000000 INFO @ Tue, 16 Jun 2020 07:27:15: 1000000 INFO @ Tue, 16 Jun 2020 07:27:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:27:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:27:18: #1 total tags in treatment: 6741609 INFO @ Tue, 16 Jun 2020 07:27:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:18: #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 07:27:18: #1 tags after filtering in treatment: 6741609 INFO @ Tue, 16 Jun 2020 07:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:19: #2 number of paired peaks: 2445 INFO @ Tue, 16 Jun 2020 07:27:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:19: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 07:27:19: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 07:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.05_model.r INFO @ Tue, 16 Jun 2020 07:27:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:27:21: 2000000 INFO @ Tue, 16 Jun 2020 07:27:26: 3000000 INFO @ Tue, 16 Jun 2020 07:27:32: 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 07:27:38: 5000000 INFO @ Tue, 16 Jun 2020 07:27:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.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 07:27:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:27:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:44: 6000000 INFO @ Tue, 16 Jun 2020 07:27:45: 1000000 INFO @ Tue, 16 Jun 2020 07:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.05_summits.bed INFO @ Tue, 16 Jun 2020 07:27:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9811 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:27:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:27:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:27:48: #1 total tags in treatment: 6741609 INFO @ Tue, 16 Jun 2020 07:27:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:48: #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 07:27:49: #1 tags after filtering in treatment: 6741609 INFO @ Tue, 16 Jun 2020 07:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:49: #2 number of paired peaks: 2445 INFO @ Tue, 16 Jun 2020 07:27:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:49: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 07:27:49: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 07:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.10_model.r INFO @ Tue, 16 Jun 2020 07:27:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:27:51: 2000000 INFO @ Tue, 16 Jun 2020 07:27:57: 3000000 INFO @ Tue, 16 Jun 2020 07:28:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:28:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:08: 5000000 INFO @ Tue, 16 Jun 2020 07:28:14: 6000000 INFO @ Tue, 16 Jun 2020 07:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.10_summits.bed INFO @ Tue, 16 Jun 2020 07:28:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7480 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:28:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:28:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:28:18: #1 total tags in treatment: 6741609 INFO @ Tue, 16 Jun 2020 07:28:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:18: #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 07:28:18: #1 tags after filtering in treatment: 6741609 INFO @ Tue, 16 Jun 2020 07:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:19: #2 number of paired peaks: 2445 INFO @ Tue, 16 Jun 2020 07:28:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:19: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 07:28:19: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 07:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.20_model.r INFO @ Tue, 16 Jun 2020 07:28:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:28:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043994/SRX043994.20_summits.bed INFO @ Tue, 16 Jun 2020 07:28:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4596 records, 4 fields): 6 millis CompletedMACS2peakCalling