Job ID = 6453485 SRX = SRX1167500 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:28:26 prefetch.2.10.7: 1) Downloading 'SRR2192589'... 2020-06-21T08:28:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:30:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:30:03 prefetch.2.10.7: 'SRR2192589' is valid 2020-06-21T08:30:03 prefetch.2.10.7: 1) 'SRR2192589' was downloaded successfully 2020-06-21T08:30:54 prefetch.2.10.7: 'SRR2192589' has 10 unresolved dependencies 2020-06-21T08:30:54 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:30:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:07 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:31:07 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:31:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:26 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:31:26 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:31:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:43 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:31:43 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:31:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:02 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:02 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:32:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:20 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:20 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:32:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:37 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:37 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:32:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:55 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:55 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:32:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:09 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:09 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:33:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:22 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:22 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:33:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:35 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 25500285 spots for SRR2192589/SRR2192589.sra Written 25500285 spots for SRR2192589/SRR2192589.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:20 25500285 reads; of these: 25500285 (100.00%) were unpaired; of these: 540966 (2.12%) aligned 0 times 20104602 (78.84%) aligned exactly 1 time 4854717 (19.04%) aligned >1 times 97.88% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 10375543 / 24959319 = 0.4157 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 17:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.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 17:44:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:12: 1000000 INFO @ Sun, 21 Jun 2020 17:44:17: 2000000 INFO @ Sun, 21 Jun 2020 17:44:23: 3000000 INFO @ Sun, 21 Jun 2020 17:44:28: 4000000 INFO @ Sun, 21 Jun 2020 17:44:33: 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 17:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.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 17:44:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:39: 6000000 INFO @ Sun, 21 Jun 2020 17:44:44: 1000000 INFO @ Sun, 21 Jun 2020 17:44:45: 7000000 INFO @ Sun, 21 Jun 2020 17:44:51: 2000000 INFO @ Sun, 21 Jun 2020 17:44:51: 8000000 INFO @ Sun, 21 Jun 2020 17:44:58: 9000000 INFO @ Sun, 21 Jun 2020 17:44:58: 3000000 INFO @ Sun, 21 Jun 2020 17:45:04: 10000000 INFO @ Sun, 21 Jun 2020 17:45:05: 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 17:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.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 17:45:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:10: 11000000 INFO @ Sun, 21 Jun 2020 17:45:12: 5000000 INFO @ Sun, 21 Jun 2020 17:45:14: 1000000 INFO @ Sun, 21 Jun 2020 17:45:17: 12000000 INFO @ Sun, 21 Jun 2020 17:45:19: 6000000 INFO @ Sun, 21 Jun 2020 17:45:21: 2000000 INFO @ Sun, 21 Jun 2020 17:45:23: 13000000 INFO @ Sun, 21 Jun 2020 17:45:26: 7000000 INFO @ Sun, 21 Jun 2020 17:45:27: 3000000 INFO @ Sun, 21 Jun 2020 17:45:29: 14000000 INFO @ Sun, 21 Jun 2020 17:45:33: 8000000 INFO @ Sun, 21 Jun 2020 17:45:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:45:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:45:33: #1 total tags in treatment: 14583776 INFO @ Sun, 21 Jun 2020 17:45:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:33: #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 17:45:34: #1 tags after filtering in treatment: 14583686 INFO @ Sun, 21 Jun 2020 17:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:34: 4000000 INFO @ Sun, 21 Jun 2020 17:45:35: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 17:45:35: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 17:45:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:35: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 17:45:35: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sun, 21 Jun 2020 17:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.05_model.r WARNING @ Sun, 21 Jun 2020 17:45:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:45:35: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sun, 21 Jun 2020 17:45:35: #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 17:45:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:40: 9000000 INFO @ Sun, 21 Jun 2020 17:45:41: 5000000 INFO @ Sun, 21 Jun 2020 17:45:47: 10000000 INFO @ Sun, 21 Jun 2020 17:45:48: 6000000 INFO @ Sun, 21 Jun 2020 17:45:54: 7000000 INFO @ Sun, 21 Jun 2020 17:45:54: 11000000 INFO @ Sun, 21 Jun 2020 17:46:01: 8000000 INFO @ Sun, 21 Jun 2020 17:46:02: 12000000 INFO @ Sun, 21 Jun 2020 17:46:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:08: 9000000 INFO @ Sun, 21 Jun 2020 17:46:09: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:46:14: 10000000 INFO @ Sun, 21 Jun 2020 17:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.05_summits.bed INFO @ Sun, 21 Jun 2020 17:46:16: Done! INFO @ Sun, 21 Jun 2020 17:46:16: 14000000 pass1 - making usageList (500 chroms): 1 millis pass2 - checking and writing primary data (2267 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:46:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:46:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:46:20: #1 total tags in treatment: 14583776 INFO @ Sun, 21 Jun 2020 17:46:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:20: #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 17:46:21: #1 tags after filtering in treatment: 14583686 INFO @ Sun, 21 Jun 2020 17:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:21: 11000000 INFO @ Sun, 21 Jun 2020 17:46:22: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 17:46:22: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 17:46:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:22: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 17:46:22: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sun, 21 Jun 2020 17:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.10_model.r WARNING @ Sun, 21 Jun 2020 17:46:22: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:22: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sun, 21 Jun 2020 17:46:22: #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 17:46:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:27: 12000000 INFO @ Sun, 21 Jun 2020 17:46:34: 13000000 INFO @ Sun, 21 Jun 2020 17:46:40: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:46:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:46:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:46:43: #1 total tags in treatment: 14583776 INFO @ Sun, 21 Jun 2020 17:46:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:43: #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 17:46:44: #1 tags after filtering in treatment: 14583686 INFO @ Sun, 21 Jun 2020 17:46:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:45: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 17:46:45: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 17:46:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:45: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 17:46:45: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sun, 21 Jun 2020 17:46:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.20_model.r WARNING @ Sun, 21 Jun 2020 17:46:45: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:45: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sun, 21 Jun 2020 17:46:45: #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 17:46:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.10_summits.bed INFO @ Sun, 21 Jun 2020 17:47:03: Done! pass1 - making usageList (296 chroms): 2 millis pass2 - checking and writing primary data (926 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167500/SRX1167500.20_summits.bed INFO @ Sun, 21 Jun 2020 17:47:27: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 7 millis CompletedMACS2peakCalling