Job ID = 6366314 SRX = SRX1099841 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:31 prefetch.2.10.7: 1) Downloading 'SRR2105913'... 2020-06-15T23:12:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:20 prefetch.2.10.7: 'SRR2105913' is valid 2020-06-15T23:13:20 prefetch.2.10.7: 1) 'SRR2105913' was downloaded successfully Read 10264029 spots for SRR2105913/SRR2105913.sra Written 10264029 spots for SRR2105913/SRR2105913.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: 00:02:15 10264029 reads; of these: 10264029 (100.00%) were unpaired; of these: 485974 (4.73%) aligned 0 times 8280372 (80.67%) aligned exactly 1 time 1497683 (14.59%) aligned >1 times 95.27% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 1317728 / 9778055 = 0.1348 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 08:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.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 08:18:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:03: 1000000 INFO @ Tue, 16 Jun 2020 08:19:08: 2000000 INFO @ Tue, 16 Jun 2020 08:19:14: 3000000 INFO @ Tue, 16 Jun 2020 08:19:20: 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 08:19:26: 5000000 INFO @ Tue, 16 Jun 2020 08:19:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.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 08:19:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:32: 6000000 INFO @ Tue, 16 Jun 2020 08:19:34: 1000000 INFO @ Tue, 16 Jun 2020 08:19:38: 7000000 INFO @ Tue, 16 Jun 2020 08:19:41: 2000000 INFO @ Tue, 16 Jun 2020 08:19:44: 8000000 INFO @ Tue, 16 Jun 2020 08:19:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:47: #1 total tags in treatment: 8460327 INFO @ Tue, 16 Jun 2020 08:19:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:47: #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 08:19:47: 3000000 INFO @ Tue, 16 Jun 2020 08:19:47: #1 tags after filtering in treatment: 8460327 INFO @ Tue, 16 Jun 2020 08:19:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:48: #2 number of paired peaks: 1010 INFO @ Tue, 16 Jun 2020 08:19:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:48: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:19:48: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 08:19:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.05_model.r INFO @ Tue, 16 Jun 2020 08:19:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:53: 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 08:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.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 08:19:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:00: 5000000 INFO @ Tue, 16 Jun 2020 08:20:03: 1000000 INFO @ Tue, 16 Jun 2020 08:20:06: 6000000 INFO @ Tue, 16 Jun 2020 08:20:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:09: 2000000 INFO @ Tue, 16 Jun 2020 08:20:13: 7000000 INFO @ Tue, 16 Jun 2020 08:20:15: 3000000 INFO @ Tue, 16 Jun 2020 08:20:19: 8000000 INFO @ Tue, 16 Jun 2020 08:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2290 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:22: 4000000 INFO @ Tue, 16 Jun 2020 08:20:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:22: #1 total tags in treatment: 8460327 INFO @ Tue, 16 Jun 2020 08:20:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:22: #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 08:20:22: #1 tags after filtering in treatment: 8460327 INFO @ Tue, 16 Jun 2020 08:20:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:23: #2 number of paired peaks: 1010 INFO @ Tue, 16 Jun 2020 08:20:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:23: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:20:23: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 08:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.10_model.r INFO @ Tue, 16 Jun 2020 08:20:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:27: 5000000 INFO @ Tue, 16 Jun 2020 08:20:33: 6000000 INFO @ Tue, 16 Jun 2020 08:20:39: 7000000 INFO @ Tue, 16 Jun 2020 08:20:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:45: 8000000 INFO @ Tue, 16 Jun 2020 08:20:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:48: #1 total tags in treatment: 8460327 INFO @ Tue, 16 Jun 2020 08:20:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:48: #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 08:20:48: #1 tags after filtering in treatment: 8460327 INFO @ Tue, 16 Jun 2020 08:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:49: #2 number of paired peaks: 1010 INFO @ Tue, 16 Jun 2020 08:20:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:49: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:20:49: #2 alternative fragment length(s) may be 4,148 bps INFO @ Tue, 16 Jun 2020 08:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.20_model.r INFO @ Tue, 16 Jun 2020 08:20:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1089 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099841/SRX1099841.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (479 records, 4 fields): 2 millis CompletedMACS2peakCalling