Job ID = 6455830 SRX = SRX3011237 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:23:06 prefetch.2.10.7: 1) Downloading 'SRR5834714'... 2020-06-21T10:23:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:35 prefetch.2.10.7: 1) 'SRR5834714' was downloaded successfully 2020-06-21T10:26:27 prefetch.2.10.7: 'SRR5834714' has 10 unresolved dependencies 2020-06-21T10:26:27 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:26:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:39 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:39 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:26:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:56 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:56 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:26:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:12 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:12 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:27:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:29 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:29 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:47 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:47 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:27:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:04 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:28:04 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:28:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:24 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:28:24 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:28:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:37 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:28:37 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:28:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:50 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:28:50 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:28:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:03 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 17790016 spots for SRR5834714/SRR5834714.sra Written 17790016 spots for SRR5834714/SRR5834714.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: 00:04:03 17790016 reads; of these: 17790016 (100.00%) were unpaired; of these: 535625 (3.01%) aligned 0 times 14770060 (83.02%) aligned exactly 1 time 2484331 (13.96%) aligned >1 times 96.99% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 8917871 / 17254391 = 0.5168 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 19:38:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.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 19:38:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:05: 1000000 INFO @ Sun, 21 Jun 2020 19:39:12: 2000000 INFO @ Sun, 21 Jun 2020 19:39:18: 3000000 INFO @ Sun, 21 Jun 2020 19:39:25: 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 19:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.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 19:39:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:32: 5000000 INFO @ Sun, 21 Jun 2020 19:39:36: 1000000 INFO @ Sun, 21 Jun 2020 19:39:39: 6000000 INFO @ Sun, 21 Jun 2020 19:39:43: 2000000 INFO @ Sun, 21 Jun 2020 19:39:46: 7000000 INFO @ Sun, 21 Jun 2020 19:39:50: 3000000 INFO @ Sun, 21 Jun 2020 19:39:53: 8000000 INFO @ Sun, 21 Jun 2020 19:39:56: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:39:56: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:39:56: #1 total tags in treatment: 8336520 INFO @ Sun, 21 Jun 2020 19:39:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:56: #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 19:39:56: #1 tags after filtering in treatment: 8336310 INFO @ Sun, 21 Jun 2020 19:39:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:56: 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 19:39:57: #2 number of paired peaks: 5499 INFO @ Sun, 21 Jun 2020 19:39:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:57: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 19:39:57: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 19:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.05_model.r INFO @ Sun, 21 Jun 2020 19:39:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.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 19:39:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:03: 5000000 INFO @ Sun, 21 Jun 2020 19:40:05: 1000000 INFO @ Sun, 21 Jun 2020 19:40:10: 6000000 INFO @ Sun, 21 Jun 2020 19:40:11: 2000000 INFO @ Sun, 21 Jun 2020 19:40:17: 3000000 INFO @ Sun, 21 Jun 2020 19:40:17: 7000000 INFO @ Sun, 21 Jun 2020 19:40:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:23: 4000000 INFO @ Sun, 21 Jun 2020 19:40:25: 8000000 INFO @ Sun, 21 Jun 2020 19:40:27: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:40:27: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:40:27: #1 total tags in treatment: 8336520 INFO @ Sun, 21 Jun 2020 19:40:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:27: #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 19:40:28: #1 tags after filtering in treatment: 8336310 INFO @ Sun, 21 Jun 2020 19:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:29: #2 number of paired peaks: 5499 INFO @ Sun, 21 Jun 2020 19:40:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:29: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 19:40:29: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 19:40:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.10_model.r INFO @ Sun, 21 Jun 2020 19:40:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:29: 5000000 INFO @ Sun, 21 Jun 2020 19:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.05_summits.bed INFO @ Sun, 21 Jun 2020 19:40:34: Done! pass1 - making usageList (236 chroms): 1 millis pass2 - checking and writing primary data (8727 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:40:35: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:40:41: 7000000 INFO @ Sun, 21 Jun 2020 19:40:47: 8000000 INFO @ Sun, 21 Jun 2020 19:40:49: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:40:49: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:40:49: #1 total tags in treatment: 8336520 INFO @ Sun, 21 Jun 2020 19:40:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:49: #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 19:40:49: #1 tags after filtering in treatment: 8336310 INFO @ Sun, 21 Jun 2020 19:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:50: #2 number of paired peaks: 5499 INFO @ Sun, 21 Jun 2020 19:40:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:50: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 19:40:50: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 19:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.20_model.r INFO @ Sun, 21 Jun 2020 19:40:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:06: Done! pass1 - making usageList (194 chroms): 2 millis pass2 - checking and writing primary data (6809 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:41:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011237/SRX3011237.20_summits.bed INFO @ Sun, 21 Jun 2020 19:41:26: Done! pass1 - making usageList (159 chroms): 2 millis pass2 - checking and writing primary data (5100 records, 4 fields): 11 millis CompletedMACS2peakCalling