Job ID = 6455847 SRX = SRX3011251 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:44:23 prefetch.2.10.7: 1) Downloading 'SRR5834728'... 2020-06-21T10:44:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:47:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:47:45 prefetch.2.10.7: 'SRR5834728' is valid 2020-06-21T10:47:45 prefetch.2.10.7: 1) 'SRR5834728' was downloaded successfully 2020-06-21T10:48:36 prefetch.2.10.7: 'SRR5834728' has 10 unresolved dependencies 2020-06-21T10:48:36 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:48:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:48:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:48:49 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:48:49 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:48:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:06 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:49:06 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:49:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:21 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:49:21 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:49:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:40 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:49:40 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:49:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:57 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:49:57 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:49:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:50:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:50:14 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:50:14 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:50:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:50:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:50:31 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:50:31 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:50:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:50:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:50:46 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:50:46 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:50:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:50:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:50:59 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:50:59 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:50:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:51:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:51:13 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 16720270 spots for SRR5834728/SRR5834728.sra Written 16720270 spots for SRR5834728/SRR5834728.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: 00:04:59 16720270 reads; of these: 16720270 (100.00%) were unpaired; of these: 286797 (1.72%) aligned 0 times 12550101 (75.06%) aligned exactly 1 time 3883372 (23.23%) aligned >1 times 98.28% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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 8 files... [bam_rmdupse_core] 5379223 / 16433473 = 0.3273 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 20:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.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 20:02:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:10: 1000000 INFO @ Sun, 21 Jun 2020 20:02:16: 2000000 INFO @ Sun, 21 Jun 2020 20:02:22: 3000000 INFO @ Sun, 21 Jun 2020 20:02:28: 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 20:02:34: 5000000 INFO @ Sun, 21 Jun 2020 20:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.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 20:02:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:40: 6000000 INFO @ Sun, 21 Jun 2020 20:02:40: 1000000 INFO @ Sun, 21 Jun 2020 20:02:46: 7000000 INFO @ Sun, 21 Jun 2020 20:02:47: 2000000 INFO @ Sun, 21 Jun 2020 20:02:53: 8000000 INFO @ Sun, 21 Jun 2020 20:02:53: 3000000 INFO @ Sun, 21 Jun 2020 20:02:59: 9000000 INFO @ Sun, 21 Jun 2020 20:02:59: 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 20:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.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 20:03:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:03:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:03:06: 10000000 INFO @ Sun, 21 Jun 2020 20:03:06: 5000000 INFO @ Sun, 21 Jun 2020 20:03:11: 1000000 INFO @ Sun, 21 Jun 2020 20:03:12: 6000000 INFO @ Sun, 21 Jun 2020 20:03:12: 11000000 INFO @ Sun, 21 Jun 2020 20:03:13: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 20:03:13: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 20:03:13: #1 total tags in treatment: 11054250 INFO @ Sun, 21 Jun 2020 20:03:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:03:13: #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 20:03:13: #1 tags after filtering in treatment: 11054133 INFO @ Sun, 21 Jun 2020 20:03:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:03:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:03:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:03:14: #2 number of paired peaks: 1840 INFO @ Sun, 21 Jun 2020 20:03:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:03:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:03:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:03:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:03:14: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 20:03:14: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 20:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.05_model.r WARNING @ Sun, 21 Jun 2020 20:03:14: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:03:14: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 20:03:14: #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 20:03:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:03:17: 2000000 INFO @ Sun, 21 Jun 2020 20:03:19: 7000000 INFO @ Sun, 21 Jun 2020 20:03:24: 3000000 INFO @ Sun, 21 Jun 2020 20:03:25: 8000000 INFO @ Sun, 21 Jun 2020 20:03:30: 4000000 INFO @ Sun, 21 Jun 2020 20:03:31: 9000000 INFO @ Sun, 21 Jun 2020 20:03:37: 5000000 INFO @ Sun, 21 Jun 2020 20:03:38: 10000000 INFO @ Sun, 21 Jun 2020 20:03:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:43: 6000000 INFO @ Sun, 21 Jun 2020 20:03:45: 11000000 INFO @ Sun, 21 Jun 2020 20:03:46: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 20:03:46: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 20:03:46: #1 total tags in treatment: 11054250 INFO @ Sun, 21 Jun 2020 20:03:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:03:46: #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 20:03:46: #1 tags after filtering in treatment: 11054133 INFO @ Sun, 21 Jun 2020 20:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:03:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:03:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:03:47: #2 number of paired peaks: 1840 INFO @ Sun, 21 Jun 2020 20:03:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:03:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:03:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:03:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:03:47: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 20:03:47: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 20:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.10_model.r WARNING @ Sun, 21 Jun 2020 20:03:47: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:03:47: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 20:03:47: #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 20:03:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:03:49: 7000000 INFO @ Sun, 21 Jun 2020 20:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.05_summits.bed INFO @ Sun, 21 Jun 2020 20:03:54: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (8565 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:03:56: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:04:02: 9000000 INFO @ Sun, 21 Jun 2020 20:04:08: 10000000 INFO @ Sun, 21 Jun 2020 20:04:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:04:15: 11000000 INFO @ Sun, 21 Jun 2020 20:04:15: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 20:04:15: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 20:04:15: #1 total tags in treatment: 11054250 INFO @ Sun, 21 Jun 2020 20:04:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:04:15: #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 20:04:15: #1 tags after filtering in treatment: 11054133 INFO @ Sun, 21 Jun 2020 20:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:04:15: #1 finished! INFO @ Sun, 21 Jun 2020 20:04:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:04:16: #2 number of paired peaks: 1840 INFO @ Sun, 21 Jun 2020 20:04:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:04:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:04:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:04:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:04:16: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 20:04:16: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 20:04:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.20_model.r WARNING @ Sun, 21 Jun 2020 20:04:16: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:04:16: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 20:04:16: #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 20:04:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:04:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.10_summits.bed INFO @ Sun, 21 Jun 2020 20:04:26: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (4784 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:04:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:04:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:04:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:04:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011251/SRX3011251.20_summits.bed INFO @ Sun, 21 Jun 2020 20:04:55: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (1919 records, 4 fields): 8 millis CompletedMACS2peakCalling