Job ID = 6365848 SRX = SRX002675 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR013610'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:11 prefetch.2.10.7: 'SRR013610' is valid 2020-06-15T23:42:11 prefetch.2.10.7: 1) 'SRR013610' was downloaded successfully Read 2500334 spots for SRR013610/SRR013610.sra Written 2500334 spots for SRR013610/SRR013610.sra 2020-06-15T23:42:29 prefetch.2.10.7: 1) Downloading 'SRR013611'... 2020-06-15T23:42:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:09 prefetch.2.10.7: 'SRR013611' is valid 2020-06-15T23:43:09 prefetch.2.10.7: 1) 'SRR013611' was downloaded successfully Read 5439836 spots for SRR013611/SRR013611.sra Written 5439836 spots for SRR013611/SRR013611.sra 2020-06-15T23:43:35 prefetch.2.10.7: 1) Downloading 'SRR013612'... 2020-06-15T23:43:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:31 prefetch.2.10.7: 'SRR013612' is valid 2020-06-15T23:44:31 prefetch.2.10.7: 1) 'SRR013612' was downloaded successfully Read 5826755 spots for SRR013612/SRR013612.sra Written 5826755 spots for SRR013612/SRR013612.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:44 13766925 reads; of these: 13766925 (100.00%) were unpaired; of these: 2346110 (17.04%) aligned 0 times 9849471 (71.54%) aligned exactly 1 time 1571344 (11.41%) aligned >1 times 82.96% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 1348103 / 11420815 = 0.1180 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 08:49:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.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 08:49:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:42: 1000000 INFO @ Tue, 16 Jun 2020 08:49:47: 2000000 INFO @ Tue, 16 Jun 2020 08:49:53: 3000000 INFO @ Tue, 16 Jun 2020 08:49:58: 4000000 INFO @ Tue, 16 Jun 2020 08:50:03: 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 08:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.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 08:50:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:09: 6000000 INFO @ Tue, 16 Jun 2020 08:50:13: 1000000 INFO @ Tue, 16 Jun 2020 08:50:14: 7000000 INFO @ Tue, 16 Jun 2020 08:50:19: 2000000 INFO @ Tue, 16 Jun 2020 08:50:20: 8000000 INFO @ Tue, 16 Jun 2020 08:50:25: 3000000 INFO @ Tue, 16 Jun 2020 08:50:25: 9000000 INFO @ Tue, 16 Jun 2020 08:50:31: 10000000 INFO @ Tue, 16 Jun 2020 08:50:31: 4000000 INFO @ Tue, 16 Jun 2020 08:50:31: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 08:50:31: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 08:50:31: #1 total tags in treatment: 10072712 INFO @ Tue, 16 Jun 2020 08:50:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:31: #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 08:50:31: #1 tags after filtering in treatment: 10072712 INFO @ Tue, 16 Jun 2020 08:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:32: #2 number of paired peaks: 882 WARNING @ Tue, 16 Jun 2020 08:50:32: Fewer paired peaks (882) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 882 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:32: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:50:32: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 08:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.05_model.r INFO @ Tue, 16 Jun 2020 08:50:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:32: #3 Pre-compute pvalue-qvalue table... 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 08:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.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 08:50:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:37: 5000000 INFO @ Tue, 16 Jun 2020 08:50:43: 1000000 INFO @ Tue, 16 Jun 2020 08:50:44: 6000000 INFO @ Tue, 16 Jun 2020 08:50:48: 2000000 INFO @ Tue, 16 Jun 2020 08:50:50: 7000000 INFO @ Tue, 16 Jun 2020 08:50:54: 3000000 INFO @ Tue, 16 Jun 2020 08:50:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:57: 8000000 INFO @ Tue, 16 Jun 2020 08:51:00: 4000000 INFO @ Tue, 16 Jun 2020 08:51:03: 9000000 INFO @ Tue, 16 Jun 2020 08:51:06: 5000000 INFO @ Tue, 16 Jun 2020 08:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.05_summits.bed INFO @ Tue, 16 Jun 2020 08:51:06: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9138 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:09: 10000000 INFO @ Tue, 16 Jun 2020 08:51:09: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 08:51:09: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 08:51:09: #1 total tags in treatment: 10072712 INFO @ Tue, 16 Jun 2020 08:51:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:09: #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 08:51:10: #1 tags after filtering in treatment: 10072712 INFO @ Tue, 16 Jun 2020 08:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:10: #2 number of paired peaks: 882 WARNING @ Tue, 16 Jun 2020 08:51:10: Fewer paired peaks (882) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 882 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:11: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:51:11: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 08:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.10_model.r INFO @ Tue, 16 Jun 2020 08:51:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:11: 6000000 INFO @ Tue, 16 Jun 2020 08:51:17: 7000000 INFO @ Tue, 16 Jun 2020 08:51:22: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:27: 9000000 INFO @ Tue, 16 Jun 2020 08:51:32: 10000000 INFO @ Tue, 16 Jun 2020 08:51:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:33: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 08:51:33: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 08:51:33: #1 total tags in treatment: 10072712 INFO @ Tue, 16 Jun 2020 08:51:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:33: #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 08:51:33: #1 tags after filtering in treatment: 10072712 INFO @ Tue, 16 Jun 2020 08:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:34: #2 number of paired peaks: 882 WARNING @ Tue, 16 Jun 2020 08:51:34: Fewer paired peaks (882) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 882 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:34: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:51:34: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 08:51:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.20_model.r INFO @ Tue, 16 Jun 2020 08:51:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6564 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX002675/SRX002675.20_summits.bed INFO @ Tue, 16 Jun 2020 08:52:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4002 records, 4 fields): 6 millis CompletedMACS2peakCalling