Job ID = 6453496 SRX = SRX1167620 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:22:17 prefetch.2.10.7: 1) Downloading 'SRR2192766'... 2020-06-21T08:22:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:44 prefetch.2.10.7: 'SRR2192766' is valid 2020-06-21T08:24:44 prefetch.2.10.7: 1) 'SRR2192766' was downloaded successfully 2020-06-21T08:25:35 prefetch.2.10.7: 'SRR2192766' has 10 unresolved dependencies 2020-06-21T08:25:35 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:25:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:25:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:25:47 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:25:47 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:25:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:25 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:26:25 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:26:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:40 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:26:40 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:26:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:00 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:27:00 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:27:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:17 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:27:17 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:27:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:33 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:27:33 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:27:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:50 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:27:50 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:27:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:04 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:28:04 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:28:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:17 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:28:17 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:28:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:30 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 21551184 spots for SRR2192766/SRR2192766.sra Written 21551184 spots for SRR2192766/SRR2192766.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: 00:04:06 21551184 reads; of these: 21551184 (100.00%) were unpaired; of these: 523216 (2.43%) aligned 0 times 17003079 (78.90%) aligned exactly 1 time 4024889 (18.68%) aligned >1 times 97.57% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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_sort_core] merging from 12 files... [bam_rmdupse_core] 8973548 / 21027968 = 0.4267 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 17:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.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 17:37:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:13: 1000000 INFO @ Sun, 21 Jun 2020 17:37:18: 2000000 INFO @ Sun, 21 Jun 2020 17:37:22: 3000000 INFO @ Sun, 21 Jun 2020 17:37:27: 4000000 INFO @ Sun, 21 Jun 2020 17:37:32: 5000000 INFO @ Sun, 21 Jun 2020 17:37:37: 6000000 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 17:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.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 17:37:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:41: 7000000 INFO @ Sun, 21 Jun 2020 17:37:43: 1000000 INFO @ Sun, 21 Jun 2020 17:37:46: 8000000 INFO @ Sun, 21 Jun 2020 17:37:48: 2000000 INFO @ Sun, 21 Jun 2020 17:37:51: 9000000 INFO @ Sun, 21 Jun 2020 17:37:53: 3000000 INFO @ Sun, 21 Jun 2020 17:37:57: 10000000 INFO @ Sun, 21 Jun 2020 17:37:58: 4000000 INFO @ Sun, 21 Jun 2020 17:38:02: 11000000 INFO @ Sun, 21 Jun 2020 17:38:03: 5000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 17:38:07: 12000000 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 17:38:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:38:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:38:07: #1 total tags in treatment: 12054420 INFO @ Sun, 21 Jun 2020 17:38:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:07: #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 17:38:07: #1 tags after filtering in treatment: 12054338 INFO @ Sun, 21 Jun 2020 17:38:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:07: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:08: 6000000 INFO @ Sun, 21 Jun 2020 17:38:08: #2 number of paired peaks: 455 WARNING @ Sun, 21 Jun 2020 17:38:08: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Sun, 21 Jun 2020 17:38:08: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.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 17:38:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:08: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:08: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:08: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:08: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:38:08: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sun, 21 Jun 2020 17:38:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.05_model.r WARNING @ Sun, 21 Jun 2020 17:38:08: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:08: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sun, 21 Jun 2020 17:38:08: #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 17:38:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:13: 7000000 INFO @ Sun, 21 Jun 2020 17:38:13: 1000000 INFO @ Sun, 21 Jun 2020 17:38:18: 8000000 INFO @ Sun, 21 Jun 2020 17:38:19: 2000000 INFO @ Sun, 21 Jun 2020 17:38:23: 9000000 INFO @ Sun, 21 Jun 2020 17:38:24: 3000000 INFO @ Sun, 21 Jun 2020 17:38:28: 10000000 INFO @ Sun, 21 Jun 2020 17:38:29: 4000000 INFO @ Sun, 21 Jun 2020 17:38:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:33: 11000000 INFO @ Sun, 21 Jun 2020 17:38:34: 5000000 INFO @ Sun, 21 Jun 2020 17:38:38: 12000000 INFO @ Sun, 21 Jun 2020 17:38:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:38:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:38:39: #1 total tags in treatment: 12054420 INFO @ Sun, 21 Jun 2020 17:38:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:39: #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 17:38:39: 6000000 INFO @ Sun, 21 Jun 2020 17:38:39: #1 tags after filtering in treatment: 12054338 INFO @ Sun, 21 Jun 2020 17:38:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:40: #2 number of paired peaks: 455 WARNING @ Sun, 21 Jun 2020 17:38:40: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Sun, 21 Jun 2020 17:38:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:40: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:38:40: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sun, 21 Jun 2020 17:38:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.10_model.r WARNING @ Sun, 21 Jun 2020 17:38:40: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:40: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sun, 21 Jun 2020 17:38:40: #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 17:38:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:43: 7000000 INFO @ Sun, 21 Jun 2020 17:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.05_summits.bed INFO @ Sun, 21 Jun 2020 17:38:44: Done! pass1 - making usageList (437 chroms): 2 millis pass2 - checking and writing primary data (1752 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:48: 8000000 INFO @ Sun, 21 Jun 2020 17:38:53: 9000000 INFO @ Sun, 21 Jun 2020 17:38:58: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:39:03: 11000000 INFO @ Sun, 21 Jun 2020 17:39:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:08: 12000000 INFO @ Sun, 21 Jun 2020 17:39:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:39:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:39:08: #1 total tags in treatment: 12054420 INFO @ Sun, 21 Jun 2020 17:39:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:08: #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 17:39:09: #1 tags after filtering in treatment: 12054338 INFO @ Sun, 21 Jun 2020 17:39:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:10: #2 number of paired peaks: 455 WARNING @ Sun, 21 Jun 2020 17:39:10: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Sun, 21 Jun 2020 17:39:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:10: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:39:10: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sun, 21 Jun 2020 17:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.20_model.r WARNING @ Sun, 21 Jun 2020 17:39:10: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:39:10: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sun, 21 Jun 2020 17:39:10: #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 17:39:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.10_summits.bed INFO @ Sun, 21 Jun 2020 17:39:15: Done! pass1 - making usageList (263 chroms): 1 millis pass2 - checking and writing primary data (776 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:39:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167620/SRX1167620.20_summits.bed INFO @ Sun, 21 Jun 2020 17:39:46: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 5 millis CompletedMACS2peakCalling