Job ID = 6457716 SRX = SRX474525 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:51:48 prefetch.2.10.7: 1) Downloading 'SRR1174372'... 2020-06-21T11:51:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:13 prefetch.2.10.7: 'SRR1174372' is valid 2020-06-21T11:52:13 prefetch.2.10.7: 1) 'SRR1174372' was downloaded successfully 2020-06-21T11:53:04 prefetch.2.10.7: 'SRR1174372' has 10 unresolved dependencies 2020-06-21T11:53:04 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T11:53:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:53:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:53:20 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:53:20 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T11:53:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:53:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:53:38 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:53:38 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T11:53:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:53:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:53:50 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:53:50 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T11:53:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:54:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:54:06 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:54:06 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T11:54:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:54:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:54:25 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:54:25 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T11:54:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:54:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:54:43 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:54:43 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T11:54:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:54:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:54:57 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:54:57 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T11:54:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:55:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:55:09 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:55:09 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T11:55:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:55:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:55:21 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:55:21 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T11:55:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:55:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:55:38 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 3086343 spots for SRR1174372/SRR1174372.sra Written 3086343 spots for SRR1174372/SRR1174372.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: 00:00:51 3086343 reads; of these: 3086343 (100.00%) were unpaired; of these: 154376 (5.00%) aligned 0 times 2015207 (65.29%) aligned exactly 1 time 916760 (29.70%) aligned >1 times 95.00% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 167955 / 2931967 = 0.0573 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 @ Sun, 21 Jun 2020 20:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:57:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:01: 1000000 INFO @ Sun, 21 Jun 2020 20:58:05: 2000000 INFO @ Sun, 21 Jun 2020 20:58:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:58:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:58:10: #1 total tags in treatment: 2764012 INFO @ Sun, 21 Jun 2020 20:58:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:58:10: #1 tags after filtering in treatment: 2763965 INFO @ Sun, 21 Jun 2020 20:58:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:10: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 20:58:10: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 20:58:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:10: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 20:58:10: #2 alternative fragment length(s) may be 61 bps INFO @ Sun, 21 Jun 2020 20:58:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.05_model.r WARNING @ Sun, 21 Jun 2020 20:58:10: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:10: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sun, 21 Jun 2020 20:58:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:58:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.05_summits.bed INFO @ Sun, 21 Jun 2020 20:58:20: Done! pass1 - making usageList (447 chroms): 1 millis pass2 - checking and writing primary data (1363 records, 4 fields): 14 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 20:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:58:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:32: 1000000 INFO @ Sun, 21 Jun 2020 20:58:38: 2000000 INFO @ Sun, 21 Jun 2020 20:58:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:58:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:58:43: #1 total tags in treatment: 2764012 INFO @ Sun, 21 Jun 2020 20:58:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:58:43: #1 tags after filtering in treatment: 2763965 INFO @ Sun, 21 Jun 2020 20:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:43: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 20:58:43: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 20:58:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:43: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 20:58:43: #2 alternative fragment length(s) may be 61 bps INFO @ Sun, 21 Jun 2020 20:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.10_model.r WARNING @ Sun, 21 Jun 2020 20:58:43: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:43: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sun, 21 Jun 2020 20:58:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:58:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.10_summits.bed INFO @ Sun, 21 Jun 2020 20:58:53: Done! 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 pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:58:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:02: 1000000 INFO @ Sun, 21 Jun 2020 20:59:07: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:59:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:59:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:59:12: #1 total tags in treatment: 2764012 INFO @ Sun, 21 Jun 2020 20:59:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:59:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:59:13: #1 tags after filtering in treatment: 2763965 INFO @ Sun, 21 Jun 2020 20:59:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:13: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 20:59:13: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 20:59:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:13: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 20:59:13: #2 alternative fragment length(s) may be 61 bps INFO @ Sun, 21 Jun 2020 20:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.20_model.r WARNING @ Sun, 21 Jun 2020 20:59:13: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:59:13: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sun, 21 Jun 2020 20:59:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:59:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:59:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474525/SRX474525.20_summits.bed INFO @ Sun, 21 Jun 2020 20:59:22: Done! pass1 - making usageList (97 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 22 millis CompletedMACS2peakCalling