Job ID = 6455132 SRX = SRX2779382 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:41 prefetch.2.10.7: 1) Downloading 'SRR5499063'... 2020-06-21T10:02:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:03:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:03:45 prefetch.2.10.7: 'SRR5499063' is valid 2020-06-21T10:03:45 prefetch.2.10.7: 1) 'SRR5499063' was downloaded successfully 2020-06-21T10:04:36 prefetch.2.10.7: 'SRR5499063' has 10 unresolved dependencies 2020-06-21T10:04:36 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:04:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:04:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:04:49 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:04:49 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:04:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:06 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:05:06 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:05:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:22 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:05:22 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:05:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:40 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:05:40 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:05:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:59 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:05:59 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:05:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:06:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:06:17 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:06:17 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:06:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:06:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:06:35 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:06:35 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:06:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:06:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:06:49 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:06:49 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:06:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:07:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:07:01 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:07:01 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:07:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:07:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:07:15 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 15150834 spots for SRR5499063/SRR5499063.sra Written 15150834 spots for SRR5499063/SRR5499063.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: 00:02:15 15150834 reads; of these: 15150834 (100.00%) were unpaired; of these: 151218 (1.00%) aligned 0 times 14793137 (97.64%) aligned exactly 1 time 206479 (1.36%) aligned >1 times 99.00% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 8744056 / 14999616 = 0.5830 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 19:13:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.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 19:13:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:25: 1000000 INFO @ Sun, 21 Jun 2020 19:13:31: 2000000 INFO @ Sun, 21 Jun 2020 19:13:37: 3000000 INFO @ Sun, 21 Jun 2020 19:13:43: 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 19:13:49: 5000000 INFO @ Sun, 21 Jun 2020 19:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.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 19:13:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:56: 6000000 INFO @ Sun, 21 Jun 2020 19:13:57: 1000000 INFO @ Sun, 21 Jun 2020 19:13:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:58: #1 total tags in treatment: 6255560 INFO @ Sun, 21 Jun 2020 19:13:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:58: #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 19:13:58: #1 tags after filtering in treatment: 6255108 INFO @ Sun, 21 Jun 2020 19:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:59: #2 number of paired peaks: 4888 INFO @ Sun, 21 Jun 2020 19:13:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:59: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 19:13:59: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 19:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.05_model.r INFO @ Sun, 21 Jun 2020 19:13:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:04: 2000000 INFO @ Sun, 21 Jun 2020 19:14:11: 3000000 INFO @ Sun, 21 Jun 2020 19:14:18: 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 19:14:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.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 19:14:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:25: 5000000 INFO @ Sun, 21 Jun 2020 19:14:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:27: Done! INFO @ Sun, 21 Jun 2020 19:14:27: 1000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6746 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:33: 6000000 INFO @ Sun, 21 Jun 2020 19:14:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:35: #1 total tags in treatment: 6255560 INFO @ Sun, 21 Jun 2020 19:14:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:35: #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 19:14:35: #1 tags after filtering in treatment: 6255108 INFO @ Sun, 21 Jun 2020 19:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:35: 2000000 INFO @ Sun, 21 Jun 2020 19:14:35: #2 number of paired peaks: 4888 INFO @ Sun, 21 Jun 2020 19:14:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:35: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 19:14:35: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 19:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.10_model.r INFO @ Sun, 21 Jun 2020 19:14:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:14:48: 4000000 INFO @ Sun, 21 Jun 2020 19:14:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:55: 5000000 INFO @ Sun, 21 Jun 2020 19:15:02: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:03: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (4925 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:04: #1 total tags in treatment: 6255560 INFO @ Sun, 21 Jun 2020 19:15:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:04: #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 19:15:04: #1 tags after filtering in treatment: 6255108 INFO @ Sun, 21 Jun 2020 19:15:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:05: #2 number of paired peaks: 4888 INFO @ Sun, 21 Jun 2020 19:15:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:05: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 19:15:05: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 19:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.20_model.r INFO @ Sun, 21 Jun 2020 19:15:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779382/SRX2779382.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:32: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (2835 records, 4 fields): 4 millis CompletedMACS2peakCalling