Job ID = 6367271 SRX = SRX330983 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:01 prefetch.2.10.7: 1) Downloading 'SRR947188'... 2020-06-15T23:23:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:25:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:25:12 prefetch.2.10.7: 1) 'SRR947188' was downloaded successfully Read 20024866 spots for SRR947188/SRR947188.sra Written 20024866 spots for SRR947188/SRR947188.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 20024866 reads; of these: 20024866 (100.00%) were unpaired; of these: 1642341 (8.20%) aligned 0 times 13197750 (65.91%) aligned exactly 1 time 5184775 (25.89%) aligned >1 times 91.80% 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] 12053520 / 18382525 = 0.6557 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 08:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.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 08:35:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:16: 1000000 INFO @ Tue, 16 Jun 2020 08:35:22: 2000000 INFO @ Tue, 16 Jun 2020 08:35:29: 3000000 INFO @ Tue, 16 Jun 2020 08:35:35: 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 08:35:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.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 08:35:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:42: 5000000 INFO @ Tue, 16 Jun 2020 08:35:47: 1000000 INFO @ Tue, 16 Jun 2020 08:35:49: 6000000 INFO @ Tue, 16 Jun 2020 08:35:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:51: #1 total tags in treatment: 6329005 INFO @ Tue, 16 Jun 2020 08:35:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:51: #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 08:35:51: #1 tags after filtering in treatment: 6329005 INFO @ Tue, 16 Jun 2020 08:35:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:52: #2 number of paired peaks: 1963 INFO @ Tue, 16 Jun 2020 08:35:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:52: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 08:35:52: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 08:35:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.05_model.r INFO @ Tue, 16 Jun 2020 08:35:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:53: 2000000 INFO @ Tue, 16 Jun 2020 08:35:59: 3000000 INFO @ Tue, 16 Jun 2020 08:36:06: 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 08:36:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.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 08:36:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:12: 5000000 INFO @ Tue, 16 Jun 2020 08:36:16: 1000000 INFO @ Tue, 16 Jun 2020 08:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5928 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:19: 6000000 INFO @ Tue, 16 Jun 2020 08:36:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:21: #1 total tags in treatment: 6329005 INFO @ Tue, 16 Jun 2020 08:36:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:21: #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 08:36:21: #1 tags after filtering in treatment: 6329005 INFO @ Tue, 16 Jun 2020 08:36:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:22: #2 number of paired peaks: 1963 INFO @ Tue, 16 Jun 2020 08:36:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:22: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 08:36:22: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 08:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.10_model.r INFO @ Tue, 16 Jun 2020 08:36:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:23: 2000000 INFO @ Tue, 16 Jun 2020 08:36:29: 3000000 INFO @ Tue, 16 Jun 2020 08:36:36: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:42: 5000000 INFO @ Tue, 16 Jun 2020 08:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:47: Done! INFO @ Tue, 16 Jun 2020 08:36:48: 6000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3498 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:50: #1 total tags in treatment: 6329005 INFO @ Tue, 16 Jun 2020 08:36:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:50: #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 08:36:50: #1 tags after filtering in treatment: 6329005 INFO @ Tue, 16 Jun 2020 08:36:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:51: #2 number of paired peaks: 1963 INFO @ Tue, 16 Jun 2020 08:36:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:51: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 08:36:51: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 08:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.20_model.r INFO @ Tue, 16 Jun 2020 08:36:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330983/SRX330983.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1952 records, 4 fields): 3 millis CompletedMACS2peakCalling