Job ID = 6453467 SRX = SRX1165009 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:17:48 prefetch.2.10.7: 1) Downloading 'SRR2188680'... 2020-06-21T08:17:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:18:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:18:15 prefetch.2.10.7: 'SRR2188680' is valid 2020-06-21T08:18:15 prefetch.2.10.7: 1) 'SRR2188680' was downloaded successfully 2020-06-21T08:19:06 prefetch.2.10.7: 'SRR2188680' has 10 unresolved dependencies 2020-06-21T08:19:06 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:19:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:19:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:19:18 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:19:18 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:19:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:19:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:19:34 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:19:34 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:19:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:19:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:19:49 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:19:49 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:19:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:20:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:20:06 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:20:06 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:20:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:20:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:20:23 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:20:23 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:20:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:20:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:20:53 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:20:53 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:20:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:12 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:21:12 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:21:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:27 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:21:27 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:21:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:40 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:21:40 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:21:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:52 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 2103919 spots for SRR2188680/SRR2188680.sra Written 2103919 spots for SRR2188680/SRR2188680.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: 00:00:37 2103919 reads; of these: 2103919 (100.00%) were unpaired; of these: 55219 (2.62%) aligned 0 times 1220041 (57.99%) aligned exactly 1 time 828659 (39.39%) aligned >1 times 97.38% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 297708 / 2048700 = 0.1453 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 17:23:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.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 17:23:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:46: 1000000 INFO @ Sun, 21 Jun 2020 17:23:51: #1 tag size is determined as 48 bps INFO @ Sun, 21 Jun 2020 17:23:51: #1 tag size = 48 INFO @ Sun, 21 Jun 2020 17:23:51: #1 total tags in treatment: 1750992 INFO @ Sun, 21 Jun 2020 17:23:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:51: #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 17:23:51: #1 tags after filtering in treatment: 1750744 INFO @ Sun, 21 Jun 2020 17:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:51: #2 number of paired peaks: 1611 INFO @ Sun, 21 Jun 2020 17:23:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:52: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 17:23:52: #2 alternative fragment length(s) may be 62 bps INFO @ Sun, 21 Jun 2020 17:23:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.05_model.r WARNING @ Sun, 21 Jun 2020 17:23:52: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:23:52: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sun, 21 Jun 2020 17:23:52: #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 17:23:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.05_summits.bed INFO @ Sun, 21 Jun 2020 17:23:58: Done! pass1 - making usageList (463 chroms): 1 millis pass2 - checking and writing primary data (1142 records, 4 fields): 13 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 17:24:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.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 17:24:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:15: 1000000 INFO @ Sun, 21 Jun 2020 17:24:20: #1 tag size is determined as 48 bps INFO @ Sun, 21 Jun 2020 17:24:20: #1 tag size = 48 INFO @ Sun, 21 Jun 2020 17:24:20: #1 total tags in treatment: 1750992 INFO @ Sun, 21 Jun 2020 17:24:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:20: #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 17:24:20: #1 tags after filtering in treatment: 1750744 INFO @ Sun, 21 Jun 2020 17:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:20: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:20: #2 number of paired peaks: 1611 INFO @ Sun, 21 Jun 2020 17:24:20: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:20: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 17:24:20: #2 alternative fragment length(s) may be 62 bps INFO @ Sun, 21 Jun 2020 17:24:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.10_model.r WARNING @ Sun, 21 Jun 2020 17:24:20: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:24:20: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sun, 21 Jun 2020 17:24:20: #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 17:24:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.10_summits.bed INFO @ Sun, 21 Jun 2020 17:24:26: Done! pass1 - making usageList (201 chroms): 1 millis pass2 - checking and writing primary data (371 records, 4 fields): 6 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 17:24:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.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 17:24:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:44: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:24:48: #1 tag size is determined as 48 bps INFO @ Sun, 21 Jun 2020 17:24:48: #1 tag size = 48 INFO @ Sun, 21 Jun 2020 17:24:48: #1 total tags in treatment: 1750992 INFO @ Sun, 21 Jun 2020 17:24:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:48: #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 17:24:49: #1 tags after filtering in treatment: 1750744 INFO @ Sun, 21 Jun 2020 17:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:49: #2 number of paired peaks: 1611 INFO @ Sun, 21 Jun 2020 17:24:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:49: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 17:24:49: #2 alternative fragment length(s) may be 62 bps INFO @ Sun, 21 Jun 2020 17:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.20_model.r WARNING @ Sun, 21 Jun 2020 17:24:49: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:24:49: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sun, 21 Jun 2020 17:24:49: #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 17:24:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:24:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1165009/SRX1165009.20_summits.bed INFO @ Sun, 21 Jun 2020 17:24:55: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 3 millis CompletedMACS2peakCalling