Job ID = 6367886 SRX = SRX4107870 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:39:44 prefetch.2.10.7: 1) Downloading 'SRR7191146'... 2020-06-15T23:39:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:46 prefetch.2.10.7: 'SRR7191146' is valid 2020-06-15T23:40:46 prefetch.2.10.7: 1) 'SRR7191146' was downloaded successfully 2020-06-15T23:41:19 prefetch.2.10.7: 'SRR7191146' has 6 unresolved dependencies 2020-06-15T23:41:19 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.5?vdb-ctx=refseq'... 2020-06-15T23:41:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:34 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:34 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.5?vdb-ctx=refseq'... 2020-06-15T23:41:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:50 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:50 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.4?vdb-ctx=refseq'... 2020-06-15T23:41:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:05 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:42:05 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.4?vdb-ctx=refseq'... 2020-06-15T23:42:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:20 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:42:20 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.5?vdb-ctx=refseq'... 2020-06-15T23:42:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:37 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:42:37 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.5?vdb-ctx=refseq'... 2020-06-15T23:42:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:58 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.5?vdb-ctx=refseq' was downloaded successfully Read 14686336 spots for SRR7191146/SRR7191146.sra Written 14686336 spots for SRR7191146/SRR7191146.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: 00:02:18 14686336 reads; of these: 14686336 (100.00%) were unpaired; of these: 1233411 (8.40%) aligned 0 times 11590492 (78.92%) aligned exactly 1 time 1862433 (12.68%) aligned >1 times 91.60% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 2167062 / 13452925 = 0.1611 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 08:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.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 08:49:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:18: 1000000 INFO @ Tue, 16 Jun 2020 08:49:24: 2000000 INFO @ Tue, 16 Jun 2020 08:49:30: 3000000 INFO @ Tue, 16 Jun 2020 08:49:35: 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 08:49:41: 5000000 INFO @ Tue, 16 Jun 2020 08:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.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 08:49:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:47: 6000000 INFO @ Tue, 16 Jun 2020 08:49:48: 1000000 INFO @ Tue, 16 Jun 2020 08:49:52: 7000000 INFO @ Tue, 16 Jun 2020 08:49:53: 2000000 INFO @ Tue, 16 Jun 2020 08:49:58: 8000000 INFO @ Tue, 16 Jun 2020 08:49:59: 3000000 INFO @ Tue, 16 Jun 2020 08:50:04: 9000000 INFO @ Tue, 16 Jun 2020 08:50:05: 4000000 INFO @ Tue, 16 Jun 2020 08:50:10: 10000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:50:11: 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 08:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.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 08:50:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:16: 11000000 INFO @ Tue, 16 Jun 2020 08:50:17: 6000000 INFO @ Tue, 16 Jun 2020 08:50:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:17: #1 total tags in treatment: 11285863 INFO @ Tue, 16 Jun 2020 08:50:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:17: #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 08:50:18: #1 tags after filtering in treatment: 11285863 INFO @ Tue, 16 Jun 2020 08:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:18: 1000000 INFO @ Tue, 16 Jun 2020 08:50:18: #2 number of paired peaks: 388 WARNING @ Tue, 16 Jun 2020 08:50:18: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:18: #2 predicted fragment length is 109 bps INFO @ Tue, 16 Jun 2020 08:50:18: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 16 Jun 2020 08:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.05_model.r INFO @ Tue, 16 Jun 2020 08:50:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:22: 7000000 INFO @ Tue, 16 Jun 2020 08:50:23: 2000000 INFO @ Tue, 16 Jun 2020 08:50:28: 3000000 INFO @ Tue, 16 Jun 2020 08:50:28: 8000000 INFO @ Tue, 16 Jun 2020 08:50:32: 4000000 INFO @ Tue, 16 Jun 2020 08:50:34: 9000000 INFO @ Tue, 16 Jun 2020 08:50:37: 5000000 INFO @ Tue, 16 Jun 2020 08:50:40: 10000000 INFO @ Tue, 16 Jun 2020 08:50:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:42: 6000000 INFO @ Tue, 16 Jun 2020 08:50:46: 11000000 INFO @ Tue, 16 Jun 2020 08:50:47: 7000000 INFO @ Tue, 16 Jun 2020 08:50:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:47: #1 total tags in treatment: 11285863 INFO @ Tue, 16 Jun 2020 08:50:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:47: #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 08:50:47: #1 tags after filtering in treatment: 11285863 INFO @ Tue, 16 Jun 2020 08:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:48: #2 number of paired peaks: 388 WARNING @ Tue, 16 Jun 2020 08:50:48: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:48: #2 predicted fragment length is 109 bps INFO @ Tue, 16 Jun 2020 08:50:48: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 16 Jun 2020 08:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.10_model.r INFO @ Tue, 16 Jun 2020 08:50:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4005 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:52: 8000000 INFO @ Tue, 16 Jun 2020 08:50:57: 9000000 INFO @ Tue, 16 Jun 2020 08:51:01: 10000000 INFO @ Tue, 16 Jun 2020 08:51:06: 11000000 INFO @ Tue, 16 Jun 2020 08:51:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:07: #1 total tags in treatment: 11285863 INFO @ Tue, 16 Jun 2020 08:51:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:07: #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 08:51:07: #1 tags after filtering in treatment: 11285863 INFO @ Tue, 16 Jun 2020 08:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:08: #2 number of paired peaks: 388 WARNING @ Tue, 16 Jun 2020 08:51:08: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:08: #2 predicted fragment length is 109 bps INFO @ Tue, 16 Jun 2020 08:51:08: #2 alternative fragment length(s) may be 109 bps INFO @ Tue, 16 Jun 2020 08:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.20_model.r INFO @ Tue, 16 Jun 2020 08:51:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2539 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107870/SRX4107870.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1098 records, 4 fields): 2 millis CompletedMACS2peakCalling