Job ID = 6367033 SRX = SRX2737092 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:31 prefetch.2.10.7: 1) Downloading 'SRR5448130'... 2020-06-15T23:14:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:05 prefetch.2.10.7: 'SRR5448130' is valid 2020-06-15T23:16:05 prefetch.2.10.7: 1) 'SRR5448130' was downloaded successfully 2020-06-15T23:16:05 prefetch.2.10.7: 'SRR5448130' has 0 unresolved dependencies Read 26611757 spots for SRR5448130/SRR5448130.sra Written 26611757 spots for SRR5448130/SRR5448130.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: 00:05:23 26611757 reads; of these: 26611757 (100.00%) were unpaired; of these: 3848601 (14.46%) aligned 0 times 19746357 (74.20%) aligned exactly 1 time 3016799 (11.34%) aligned >1 times 85.54% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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 12 files... [bam_rmdupse_core] 8189330 / 22763156 = 0.3598 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 08:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.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 08:26:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:59: 1000000 INFO @ Tue, 16 Jun 2020 08:27:04: 2000000 INFO @ Tue, 16 Jun 2020 08:27:09: 3000000 INFO @ Tue, 16 Jun 2020 08:27:15: 4000000 INFO @ Tue, 16 Jun 2020 08:27:20: 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 08:27:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.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 08:27:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:26: 6000000 INFO @ Tue, 16 Jun 2020 08:27:29: 1000000 INFO @ Tue, 16 Jun 2020 08:27:32: 7000000 INFO @ Tue, 16 Jun 2020 08:27:35: 2000000 INFO @ Tue, 16 Jun 2020 08:27:38: 8000000 INFO @ Tue, 16 Jun 2020 08:27:41: 3000000 INFO @ Tue, 16 Jun 2020 08:27:44: 9000000 INFO @ Tue, 16 Jun 2020 08:27:47: 4000000 INFO @ Tue, 16 Jun 2020 08:27:50: 10000000 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 08:27:53: 5000000 INFO @ Tue, 16 Jun 2020 08:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.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 08:27:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:56: 11000000 INFO @ Tue, 16 Jun 2020 08:27:59: 6000000 INFO @ Tue, 16 Jun 2020 08:28:00: 1000000 INFO @ Tue, 16 Jun 2020 08:28:02: 12000000 INFO @ Tue, 16 Jun 2020 08:28:06: 7000000 INFO @ Tue, 16 Jun 2020 08:28:06: 2000000 INFO @ Tue, 16 Jun 2020 08:28:09: 13000000 INFO @ Tue, 16 Jun 2020 08:28:12: 8000000 INFO @ Tue, 16 Jun 2020 08:28:13: 3000000 INFO @ Tue, 16 Jun 2020 08:28:15: 14000000 INFO @ Tue, 16 Jun 2020 08:28:19: 9000000 INFO @ Tue, 16 Jun 2020 08:28:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:19: #1 total tags in treatment: 14573826 INFO @ Tue, 16 Jun 2020 08:28:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:19: #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 08:28:19: 4000000 INFO @ Tue, 16 Jun 2020 08:28:19: #1 tags after filtering in treatment: 14573826 INFO @ Tue, 16 Jun 2020 08:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:20: #2 number of paired peaks: 1895 INFO @ Tue, 16 Jun 2020 08:28:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:21: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:28:21: #2 alternative fragment length(s) may be 4,165 bps INFO @ Tue, 16 Jun 2020 08:28:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.05_model.r INFO @ Tue, 16 Jun 2020 08:28:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:25: 10000000 INFO @ Tue, 16 Jun 2020 08:28:26: 5000000 INFO @ Tue, 16 Jun 2020 08:28:31: 11000000 INFO @ Tue, 16 Jun 2020 08:28:32: 6000000 INFO @ Tue, 16 Jun 2020 08:28:38: 12000000 INFO @ Tue, 16 Jun 2020 08:28:38: 7000000 INFO @ Tue, 16 Jun 2020 08:28:44: 13000000 INFO @ Tue, 16 Jun 2020 08:28:44: 8000000 INFO @ Tue, 16 Jun 2020 08:28:50: 14000000 INFO @ Tue, 16 Jun 2020 08:28:51: 9000000 INFO @ Tue, 16 Jun 2020 08:28:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:54: #1 total tags in treatment: 14573826 INFO @ Tue, 16 Jun 2020 08:28:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:54: #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 08:28:54: #1 tags after filtering in treatment: 14573826 INFO @ Tue, 16 Jun 2020 08:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:55: #2 number of paired peaks: 1895 INFO @ Tue, 16 Jun 2020 08:28:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:55: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:28:55: #2 alternative fragment length(s) may be 4,165 bps INFO @ Tue, 16 Jun 2020 08:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.10_model.r INFO @ Tue, 16 Jun 2020 08:28:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:57: 10000000 INFO @ Tue, 16 Jun 2020 08:29:02: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:08: 12000000 INFO @ Tue, 16 Jun 2020 08:29:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.05_summits.bed INFO @ Tue, 16 Jun 2020 08:29:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6705 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:13: 13000000 INFO @ Tue, 16 Jun 2020 08:29:19: 14000000 INFO @ Tue, 16 Jun 2020 08:29:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:29:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:29:22: #1 total tags in treatment: 14573826 INFO @ Tue, 16 Jun 2020 08:29:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:22: #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 08:29:22: #1 tags after filtering in treatment: 14573826 INFO @ Tue, 16 Jun 2020 08:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:23: #2 number of paired peaks: 1895 INFO @ Tue, 16 Jun 2020 08:29:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:24: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:29:24: #2 alternative fragment length(s) may be 4,165 bps INFO @ Tue, 16 Jun 2020 08:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.20_model.r INFO @ Tue, 16 Jun 2020 08:29:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3927 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737092/SRX2737092.20_summits.bed INFO @ Tue, 16 Jun 2020 08:30:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1665 records, 4 fields): 3 millis CompletedMACS2peakCalling