Job ID = 6453489 SRX = SRX1167591 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 'SRR2192666'... 2020-06-21T08:22:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:20 prefetch.2.10.7: 'SRR2192666' is valid 2020-06-21T08:24:20 prefetch.2.10.7: 1) 'SRR2192666' was downloaded successfully 2020-06-21T08:25:11 prefetch.2.10.7: 'SRR2192666' has 10 unresolved dependencies 2020-06-21T08:25:11 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:25:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:25:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:25:23 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:25:23 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:25:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:25:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:25:39 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:25:39 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:25:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:25:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:25:54 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:25:54 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:25:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:12 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:26:12 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:26:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:32 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:26:32 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:26:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:48 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:26:48 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:26:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:08 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:27:08 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:27:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:22 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:27:22 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:27:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:35 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:27:35 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:27:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:48 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 22122681 spots for SRR2192666/SRR2192666.sra Written 22122681 spots for SRR2192666/SRR2192666.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: 00:04:40 22122681 reads; of these: 22122681 (100.00%) were unpaired; of these: 479092 (2.17%) aligned 0 times 17551114 (79.34%) aligned exactly 1 time 4092475 (18.50%) aligned >1 times 97.83% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 9180684 / 21643589 = 0.4242 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 17:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.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 17:37:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:25: 1000000 INFO @ Sun, 21 Jun 2020 17:37:30: 2000000 INFO @ Sun, 21 Jun 2020 17:37:36: 3000000 INFO @ Sun, 21 Jun 2020 17:37:41: 4000000 INFO @ Sun, 21 Jun 2020 17:37:47: 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 @ Sun, 21 Jun 2020 17:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.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 17:37:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:53: 6000000 INFO @ Sun, 21 Jun 2020 17:37:56: 1000000 INFO @ Sun, 21 Jun 2020 17:37:59: 7000000 INFO @ Sun, 21 Jun 2020 17:38:02: 2000000 INFO @ Sun, 21 Jun 2020 17:38:06: 8000000 INFO @ Sun, 21 Jun 2020 17:38:09: 3000000 INFO @ Sun, 21 Jun 2020 17:38:12: 9000000 INFO @ Sun, 21 Jun 2020 17:38:15: 4000000 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 17:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.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 17:38:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:19: 10000000 INFO @ Sun, 21 Jun 2020 17:38:22: 5000000 INFO @ Sun, 21 Jun 2020 17:38:27: 11000000 INFO @ Sun, 21 Jun 2020 17:38:27: 1000000 INFO @ Sun, 21 Jun 2020 17:38:29: 6000000 INFO @ Sun, 21 Jun 2020 17:38:34: 12000000 INFO @ Sun, 21 Jun 2020 17:38:34: 2000000 INFO @ Sun, 21 Jun 2020 17:38:37: 7000000 INFO @ Sun, 21 Jun 2020 17:38:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:38:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:38:38: #1 total tags in treatment: 12462905 INFO @ Sun, 21 Jun 2020 17:38:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:38: #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 17:38:38: #1 tags after filtering in treatment: 12462799 INFO @ Sun, 21 Jun 2020 17:38:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:38: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:39: #2 number of paired peaks: 377 WARNING @ Sun, 21 Jun 2020 17:38:39: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sun, 21 Jun 2020 17:38:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:39: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:38:39: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 17:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.05_model.r WARNING @ Sun, 21 Jun 2020 17:38:39: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:39: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 17:38:39: #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 17:38:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:42: 3000000 INFO @ Sun, 21 Jun 2020 17:38:44: 8000000 INFO @ Sun, 21 Jun 2020 17:38:50: 4000000 INFO @ Sun, 21 Jun 2020 17:38:52: 9000000 INFO @ Sun, 21 Jun 2020 17:38:58: 5000000 INFO @ Sun, 21 Jun 2020 17:39:00: 10000000 INFO @ Sun, 21 Jun 2020 17:39:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:06: 6000000 INFO @ Sun, 21 Jun 2020 17:39:07: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:39:14: 7000000 INFO @ Sun, 21 Jun 2020 17:39:15: 12000000 INFO @ Sun, 21 Jun 2020 17:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.05_summits.bed INFO @ Sun, 21 Jun 2020 17:39:16: Done! pass1 - making usageList (448 chroms): 1 millis pass2 - checking and writing primary data (1607 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:39:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:39:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:39:19: #1 total tags in treatment: 12462905 INFO @ Sun, 21 Jun 2020 17:39:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:19: #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 17:39:19: #1 tags after filtering in treatment: 12462799 INFO @ Sun, 21 Jun 2020 17:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:19: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:20: #2 number of paired peaks: 377 WARNING @ Sun, 21 Jun 2020 17:39:20: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sun, 21 Jun 2020 17:39:20: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:20: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:39:20: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 17:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.10_model.r WARNING @ Sun, 21 Jun 2020 17:39:20: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:39:20: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 17:39:20: #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 17:39:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:22: 8000000 INFO @ Sun, 21 Jun 2020 17:39:29: 9000000 INFO @ Sun, 21 Jun 2020 17:39:36: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:39:43: 11000000 INFO @ Sun, 21 Jun 2020 17:39:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:50: 12000000 INFO @ Sun, 21 Jun 2020 17:39:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:39:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:39:53: #1 total tags in treatment: 12462905 INFO @ Sun, 21 Jun 2020 17:39:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:53: #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 17:39:53: #1 tags after filtering in treatment: 12462799 INFO @ Sun, 21 Jun 2020 17:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:54: #2 number of paired peaks: 377 WARNING @ Sun, 21 Jun 2020 17:39:54: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sun, 21 Jun 2020 17:39:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:54: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:39:54: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 17:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.20_model.r WARNING @ Sun, 21 Jun 2020 17:39:54: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:39:54: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 17:39:54: #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 17:39:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.10_summits.bed INFO @ Sun, 21 Jun 2020 17:39:58: Done! pass1 - making usageList (266 chroms): 1 millis pass2 - checking and writing primary data (723 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:40:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167591/SRX1167591.20_summits.bed INFO @ Sun, 21 Jun 2020 17:40:32: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 5 millis CompletedMACS2peakCalling