Job ID = 6454214 SRX = SRX191910 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:58:04 prefetch.2.10.7: 1) Downloading 'SRR580340'... 2020-06-21T08:58:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:04 prefetch.2.10.7: 'SRR580340' is valid 2020-06-21T09:00:04 prefetch.2.10.7: 1) 'SRR580340' was downloaded successfully Read 11994514 spots for SRR580340/SRR580340.sra Written 11994514 spots for SRR580340/SRR580340.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: 00:02:24 11994514 reads; of these: 11994514 (100.00%) were unpaired; of these: 3039185 (25.34%) aligned 0 times 8044184 (67.07%) aligned exactly 1 time 911145 (7.60%) aligned >1 times 74.66% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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_rmdupse_core] 4890530 / 8955329 = 0.5461 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 18:05:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.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 18:05:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:43: 1000000 INFO @ Sun, 21 Jun 2020 18:05:49: 2000000 INFO @ Sun, 21 Jun 2020 18:05:56: 3000000 INFO @ Sun, 21 Jun 2020 18:06:03: 4000000 INFO @ Sun, 21 Jun 2020 18:06:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:06:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:06:03: #1 total tags in treatment: 4064799 INFO @ Sun, 21 Jun 2020 18:06:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:03: #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 18:06:04: #1 tags after filtering in treatment: 4064473 INFO @ Sun, 21 Jun 2020 18:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:04: #2 number of paired peaks: 4764 INFO @ Sun, 21 Jun 2020 18:06:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:04: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 18:06:04: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 18:06:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.05_model.r INFO @ Sun, 21 Jun 2020 18:06:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:04: #3 Pre-compute pvalue-qvalue table... 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 18:06:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.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 18:06:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:13: 1000000 INFO @ Sun, 21 Jun 2020 18:06:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:06:19: 2000000 INFO @ Sun, 21 Jun 2020 18:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:06:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.05_summits.bed INFO @ Sun, 21 Jun 2020 18:06:21: Done! pass1 - making usageList (191 chroms): 1 millis pass2 - checking and writing primary data (6349 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:06:26: 3000000 INFO @ Sun, 21 Jun 2020 18:06:32: 4000000 INFO @ Sun, 21 Jun 2020 18:06:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:06:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:06:33: #1 total tags in treatment: 4064799 INFO @ Sun, 21 Jun 2020 18:06:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:33: #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 18:06:33: #1 tags after filtering in treatment: 4064473 INFO @ Sun, 21 Jun 2020 18:06:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:34: #2 number of paired peaks: 4764 INFO @ Sun, 21 Jun 2020 18:06:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:34: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 18:06:34: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 18:06:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.10_model.r INFO @ Sun, 21 Jun 2020 18:06:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:34: #3 Pre-compute pvalue-qvalue table... 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 18:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.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 18:06:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:43: 1000000 INFO @ Sun, 21 Jun 2020 18:06:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:06:50: 2000000 INFO @ Sun, 21 Jun 2020 18:06:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:06:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:06:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.10_summits.bed INFO @ Sun, 21 Jun 2020 18:06:51: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (4993 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:06:57: 3000000 INFO @ Sun, 21 Jun 2020 18:07:04: 4000000 INFO @ Sun, 21 Jun 2020 18:07:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:07:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:07:04: #1 total tags in treatment: 4064799 INFO @ Sun, 21 Jun 2020 18:07:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:07:05: #1 tags after filtering in treatment: 4064473 INFO @ Sun, 21 Jun 2020 18:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:05: #2 number of paired peaks: 4764 INFO @ Sun, 21 Jun 2020 18:07:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:05: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 18:07:05: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 18:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.20_model.r INFO @ Sun, 21 Jun 2020 18:07:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191910/SRX191910.20_summits.bed INFO @ Sun, 21 Jun 2020 18:07:22: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (4023 records, 4 fields): 8 millis CompletedMACS2peakCalling