Job ID = 6498654 SRX = SRX661499 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:59:04 prefetch.2.10.7: 1) Downloading 'SRR1525219'... 2020-06-25T23:59:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:59:40 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:59:41 prefetch.2.10.7: 'SRR1525219' is valid 2020-06-25T23:59:41 prefetch.2.10.7: 1) 'SRR1525219' was downloaded successfully 2020-06-26T00:00:32 prefetch.2.10.7: 'SRR1525219' has 10 unresolved dependencies 2020-06-26T00:00:32 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-26T00:00:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:00:47 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:00:47 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:00:47 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-26T00:00:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:01:05 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:01:05 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:01:05 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-26T00:01:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:01:17 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:01:17 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:01:17 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-26T00:01:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:01:31 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:01:31 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:01:31 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-26T00:01:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:01:52 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:01:52 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:01:52 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-26T00:01:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:09 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:09 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:02:09 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-26T00:02:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:23 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:02:23 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-26T00:02:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:35 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:35 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:02:35 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-26T00:02:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:50 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-26T00:02:50 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-26T00:02:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:03:05 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:03:05 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 7994797 spots for SRR1525219/SRR1525219.sra Written 7994797 spots for SRR1525219/SRR1525219.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: 00:01:16 7994797 reads; of these: 7994797 (100.00%) were unpaired; of these: 82492 (1.03%) aligned 0 times 7831508 (97.96%) aligned exactly 1 time 80797 (1.01%) aligned >1 times 98.97% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 461 / 7912305 = 0.0001 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 @ Fri, 26 Jun 2020 09:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.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 @ Fri, 26 Jun 2020 09:07:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:07:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:07:07: 1000000 INFO @ Fri, 26 Jun 2020 09:07:14: 2000000 INFO @ Fri, 26 Jun 2020 09:07:20: 3000000 INFO @ Fri, 26 Jun 2020 09:07:27: 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 @ Fri, 26 Jun 2020 09:07:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.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 @ Fri, 26 Jun 2020 09:07:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:07:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:07:33: 5000000 INFO @ Fri, 26 Jun 2020 09:07:37: 1000000 INFO @ Fri, 26 Jun 2020 09:07:40: 6000000 INFO @ Fri, 26 Jun 2020 09:07:44: 2000000 INFO @ Fri, 26 Jun 2020 09:07:47: 7000000 INFO @ Fri, 26 Jun 2020 09:07:50: 3000000 INFO @ Fri, 26 Jun 2020 09:07:54: #1 tag size is determined as 47 bps INFO @ Fri, 26 Jun 2020 09:07:54: #1 tag size = 47 INFO @ Fri, 26 Jun 2020 09:07:54: #1 total tags in treatment: 7911844 INFO @ Fri, 26 Jun 2020 09:07:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:07:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:07:54: #1 tags after filtering in treatment: 7911844 INFO @ Fri, 26 Jun 2020 09:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:07:54: #1 finished! INFO @ Fri, 26 Jun 2020 09:07:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:07:55: #2 number of paired peaks: 8116 INFO @ Fri, 26 Jun 2020 09:07:55: start model_add_line... INFO @ Fri, 26 Jun 2020 09:07:55: start X-correlation... INFO @ Fri, 26 Jun 2020 09:07:55: end of X-cor INFO @ Fri, 26 Jun 2020 09:07:55: #2 finished! INFO @ Fri, 26 Jun 2020 09:07:55: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 09:07:55: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 26 Jun 2020 09:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.05_model.r INFO @ Fri, 26 Jun 2020 09:07:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:07:57: 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 @ Fri, 26 Jun 2020 09:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.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 @ Fri, 26 Jun 2020 09:08:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:08:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:08:03: 5000000 INFO @ Fri, 26 Jun 2020 09:08:08: 1000000 INFO @ Fri, 26 Jun 2020 09:08:09: 6000000 INFO @ Fri, 26 Jun 2020 09:08:15: 2000000 INFO @ Fri, 26 Jun 2020 09:08:16: 7000000 INFO @ Fri, 26 Jun 2020 09:08:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:08:22: #1 tag size is determined as 47 bps INFO @ Fri, 26 Jun 2020 09:08:22: #1 tag size = 47 INFO @ Fri, 26 Jun 2020 09:08:22: #1 total tags in treatment: 7911844 INFO @ Fri, 26 Jun 2020 09:08:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:08:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:08:22: #1 tags after filtering in treatment: 7911844 INFO @ Fri, 26 Jun 2020 09:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:08:22: #1 finished! INFO @ Fri, 26 Jun 2020 09:08:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:08:22: 3000000 INFO @ Fri, 26 Jun 2020 09:08:23: #2 number of paired peaks: 8116 INFO @ Fri, 26 Jun 2020 09:08:23: start model_add_line... INFO @ Fri, 26 Jun 2020 09:08:23: start X-correlation... INFO @ Fri, 26 Jun 2020 09:08:23: end of X-cor INFO @ Fri, 26 Jun 2020 09:08:23: #2 finished! INFO @ Fri, 26 Jun 2020 09:08:23: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 09:08:23: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 26 Jun 2020 09:08:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.10_model.r INFO @ Fri, 26 Jun 2020 09:08:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:08:29: 4000000 INFO @ Fri, 26 Jun 2020 09:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.05_summits.bed INFO @ Fri, 26 Jun 2020 09:08:30: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6621 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:08:36: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:08:42: 6000000 INFO @ Fri, 26 Jun 2020 09:08:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:08:49: 7000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:08:55: #1 tag size is determined as 47 bps INFO @ Fri, 26 Jun 2020 09:08:55: #1 tag size = 47 INFO @ Fri, 26 Jun 2020 09:08:55: #1 total tags in treatment: 7911844 INFO @ Fri, 26 Jun 2020 09:08:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:08:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:08:55: #1 tags after filtering in treatment: 7911844 INFO @ Fri, 26 Jun 2020 09:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:08:55: #1 finished! INFO @ Fri, 26 Jun 2020 09:08:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.10_summits.bed INFO @ Fri, 26 Jun 2020 09:08:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6334 records, 4 fields): 8 millis INFO @ Fri, 26 Jun 2020 09:08:56: #2 number of paired peaks: 8116 INFO @ Fri, 26 Jun 2020 09:08:56: start model_add_line... CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:08:56: start X-correlation... INFO @ Fri, 26 Jun 2020 09:08:56: end of X-cor INFO @ Fri, 26 Jun 2020 09:08:56: #2 finished! INFO @ Fri, 26 Jun 2020 09:08:56: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 09:08:56: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 26 Jun 2020 09:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.20_model.r INFO @ Fri, 26 Jun 2020 09:08:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:09:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:09:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:09:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:09:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661499/SRX661499.20_summits.bed INFO @ Fri, 26 Jun 2020 09:09:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5829 records, 4 fields): 8 millis CompletedMACS2peakCalling