Job ID = 6453499 SRX = SRX1167622 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:28:57 prefetch.2.10.7: 1) Downloading 'SRR2192794'... 2020-06-21T08:28:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:36 prefetch.2.10.7: 'SRR2192794' is valid 2020-06-21T08:31:36 prefetch.2.10.7: 1) 'SRR2192794' was downloaded successfully 2020-06-21T08:32:27 prefetch.2.10.7: 'SRR2192794' has 10 unresolved dependencies 2020-06-21T08:32:27 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:32:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:39 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:39 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:32:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:56 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:56 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:32:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:12 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:12 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:33:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:31 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:31 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:33:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:49 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:49 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:33:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:34:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:34:06 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:34:06 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:34:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:34:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:34:25 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:34:25 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:34:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:34:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:34:38 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:34:38 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:34:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:34:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:34:52 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:34:52 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:34:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:35:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:35:05 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 28391159 spots for SRR2192794/SRR2192794.sra Written 28391159 spots for SRR2192794/SRR2192794.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: 00:05:48 28391159 reads; of these: 28391159 (100.00%) were unpaired; of these: 686717 (2.42%) aligned 0 times 22119737 (77.91%) aligned exactly 1 time 5584705 (19.67%) aligned >1 times 97.58% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 14684593 / 27704442 = 0.5300 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 17:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.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 17:46:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:03: 1000000 INFO @ Sun, 21 Jun 2020 17:47:10: 2000000 INFO @ Sun, 21 Jun 2020 17:47:17: 3000000 INFO @ Sun, 21 Jun 2020 17:47:24: 4000000 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 17:47:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.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 17:47:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:32: 5000000 INFO @ Sun, 21 Jun 2020 17:47:34: 1000000 INFO @ Sun, 21 Jun 2020 17:47:39: 6000000 INFO @ Sun, 21 Jun 2020 17:47:41: 2000000 INFO @ Sun, 21 Jun 2020 17:47:47: 7000000 INFO @ Sun, 21 Jun 2020 17:47:49: 3000000 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 17:47:55: 8000000 INFO @ Sun, 21 Jun 2020 17:47:57: 4000000 INFO @ Sun, 21 Jun 2020 17:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.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 17:47:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:03: 9000000 INFO @ Sun, 21 Jun 2020 17:48:04: 5000000 INFO @ Sun, 21 Jun 2020 17:48:04: 1000000 INFO @ Sun, 21 Jun 2020 17:48:11: 10000000 INFO @ Sun, 21 Jun 2020 17:48:12: 6000000 INFO @ Sun, 21 Jun 2020 17:48:12: 2000000 INFO @ Sun, 21 Jun 2020 17:48:19: 11000000 INFO @ Sun, 21 Jun 2020 17:48:19: 7000000 INFO @ Sun, 21 Jun 2020 17:48:20: 3000000 INFO @ Sun, 21 Jun 2020 17:48:27: 12000000 INFO @ Sun, 21 Jun 2020 17:48:27: 8000000 INFO @ Sun, 21 Jun 2020 17:48:27: 4000000 INFO @ Sun, 21 Jun 2020 17:48:35: 9000000 INFO @ Sun, 21 Jun 2020 17:48:35: 13000000 INFO @ Sun, 21 Jun 2020 17:48:35: 5000000 INFO @ Sun, 21 Jun 2020 17:48:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:48:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:48:35: #1 total tags in treatment: 13019849 INFO @ Sun, 21 Jun 2020 17:48:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:35: #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 17:48:36: #1 tags after filtering in treatment: 13019762 INFO @ Sun, 21 Jun 2020 17:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:37: #2 number of paired peaks: 516 WARNING @ Sun, 21 Jun 2020 17:48:37: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:37: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:37: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:37: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 17:48:37: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 17:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.05_model.r WARNING @ Sun, 21 Jun 2020 17:48:37: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:48:37: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 17:48:37: #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 17:48:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:42: 10000000 INFO @ Sun, 21 Jun 2020 17:48:42: 6000000 INFO @ Sun, 21 Jun 2020 17:48:49: 11000000 INFO @ Sun, 21 Jun 2020 17:48:50: 7000000 INFO @ Sun, 21 Jun 2020 17:48:56: 12000000 INFO @ Sun, 21 Jun 2020 17:48:57: 8000000 INFO @ Sun, 21 Jun 2020 17:49:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:04: 13000000 INFO @ Sun, 21 Jun 2020 17:49:04: 9000000 INFO @ Sun, 21 Jun 2020 17:49:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:49:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:49:04: #1 total tags in treatment: 13019849 INFO @ Sun, 21 Jun 2020 17:49:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:04: #1 tags after filtering in treatment: 13019762 INFO @ Sun, 21 Jun 2020 17:49:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:05: #2 number of paired peaks: 516 WARNING @ Sun, 21 Jun 2020 17:49:05: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sun, 21 Jun 2020 17:49:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:05: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 17:49:05: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 17:49:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.10_model.r WARNING @ Sun, 21 Jun 2020 17:49:05: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:05: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 17:49:05: #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 17:49:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:10: 10000000 INFO @ Sun, 21 Jun 2020 17:49:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:14: Done! pass1 - making usageList (544 chroms): 2 millis pass2 - checking and writing primary data (2470 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:17: 11000000 INFO @ Sun, 21 Jun 2020 17:49:23: 12000000 INFO @ Sun, 21 Jun 2020 17:49:29: 13000000 INFO @ Sun, 21 Jun 2020 17:49:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:49:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:49:29: #1 total tags in treatment: 13019849 INFO @ Sun, 21 Jun 2020 17:49:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:29: #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 17:49:29: #1 tags after filtering in treatment: 13019762 INFO @ Sun, 21 Jun 2020 17:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:30: #2 number of paired peaks: 516 WARNING @ Sun, 21 Jun 2020 17:49:30: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sun, 21 Jun 2020 17:49:30: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:30: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 17:49:30: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 17:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.20_model.r WARNING @ Sun, 21 Jun 2020 17:49:30: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:30: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 17:49:30: #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 17:49:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.10_summits.bed INFO @ Sun, 21 Jun 2020 17:49:46: Done! pass1 - making usageList (395 chroms): 1 millis pass2 - checking and writing primary data (1145 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167622/SRX1167622.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:11: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 7 millis CompletedMACS2peakCalling