Job ID = 6368979 SRX = SRX7971804 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:38:05 prefetch.2.10.7: 1) Downloading 'SRR11392690'... 2020-06-16T00:38:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:58 prefetch.2.10.7: 1) 'SRR11392690' was downloaded successfully Read 20409844 spots for SRR11392690/SRR11392690.sra Written 20409844 spots for SRR11392690/SRR11392690.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: 00:05:04 20409844 reads; of these: 20409844 (100.00%) were unpaired; of these: 7006553 (34.33%) aligned 0 times 11885851 (58.24%) aligned exactly 1 time 1517440 (7.43%) aligned >1 times 65.67% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 3394943 / 13403291 = 0.2533 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 09:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.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 09:52:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:11: 1000000 INFO @ Tue, 16 Jun 2020 09:52:18: 2000000 INFO @ Tue, 16 Jun 2020 09:52:25: 3000000 INFO @ Tue, 16 Jun 2020 09:52:32: 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 09:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.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 09:52:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:40: 5000000 INFO @ Tue, 16 Jun 2020 09:52:45: 1000000 INFO @ Tue, 16 Jun 2020 09:52:49: 6000000 INFO @ Tue, 16 Jun 2020 09:52:56: 2000000 INFO @ Tue, 16 Jun 2020 09:52:58: 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 09:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.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 09:53:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:07: 8000000 INFO @ Tue, 16 Jun 2020 09:53:07: 3000000 INFO @ Tue, 16 Jun 2020 09:53:15: 1000000 INFO @ Tue, 16 Jun 2020 09:53:16: 9000000 INFO @ Tue, 16 Jun 2020 09:53:18: 4000000 INFO @ Tue, 16 Jun 2020 09:53:26: 2000000 INFO @ Tue, 16 Jun 2020 09:53:26: 10000000 INFO @ Tue, 16 Jun 2020 09:53:26: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:53:26: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:53:26: #1 total tags in treatment: 10008348 INFO @ Tue, 16 Jun 2020 09:53:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:26: #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 09:53:26: #1 tags after filtering in treatment: 10008348 INFO @ Tue, 16 Jun 2020 09:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:27: #2 number of paired peaks: 4077 INFO @ Tue, 16 Jun 2020 09:53:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:27: #2 predicted fragment length is 184 bps INFO @ Tue, 16 Jun 2020 09:53:27: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 16 Jun 2020 09:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.05_model.r INFO @ Tue, 16 Jun 2020 09:53:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:29: 5000000 INFO @ Tue, 16 Jun 2020 09:53:36: 3000000 INFO @ Tue, 16 Jun 2020 09:53:39: 6000000 INFO @ Tue, 16 Jun 2020 09:53:46: 4000000 INFO @ Tue, 16 Jun 2020 09:53:49: 7000000 INFO @ Tue, 16 Jun 2020 09:53:55: 5000000 INFO @ Tue, 16 Jun 2020 09:53:56: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:59: 8000000 INFO @ Tue, 16 Jun 2020 09:54:05: 6000000 INFO @ Tue, 16 Jun 2020 09:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.05_summits.bed INFO @ Tue, 16 Jun 2020 09:54:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (13315 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:10: 9000000 INFO @ Tue, 16 Jun 2020 09:54:14: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:19: 10000000 INFO @ Tue, 16 Jun 2020 09:54:20: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:54:20: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:54:20: #1 total tags in treatment: 10008348 INFO @ Tue, 16 Jun 2020 09:54:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:20: #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 09:54:20: #1 tags after filtering in treatment: 10008348 INFO @ Tue, 16 Jun 2020 09:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:21: #2 number of paired peaks: 4077 INFO @ Tue, 16 Jun 2020 09:54:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:21: #2 predicted fragment length is 184 bps INFO @ Tue, 16 Jun 2020 09:54:21: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 16 Jun 2020 09:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.10_model.r INFO @ Tue, 16 Jun 2020 09:54:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:23: 8000000 INFO @ Tue, 16 Jun 2020 09:54:31: 9000000 INFO @ Tue, 16 Jun 2020 09:54:39: 10000000 INFO @ Tue, 16 Jun 2020 09:54:39: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:54:39: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:54:39: #1 total tags in treatment: 10008348 INFO @ Tue, 16 Jun 2020 09:54:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:39: #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 09:54:39: #1 tags after filtering in treatment: 10008348 INFO @ Tue, 16 Jun 2020 09:54:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:40: #2 number of paired peaks: 4077 INFO @ Tue, 16 Jun 2020 09:54:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:41: #2 predicted fragment length is 184 bps INFO @ Tue, 16 Jun 2020 09:54:41: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 16 Jun 2020 09:54:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.20_model.r INFO @ Tue, 16 Jun 2020 09:54:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9420 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971804/SRX7971804.20_summits.bed INFO @ Tue, 16 Jun 2020 09:55:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5107 records, 4 fields): 6 millis CompletedMACS2peakCalling