Job ID = 6457071 SRX = SRX4375835 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:32:10 prefetch.2.10.7: 1) Downloading 'SRR7506489'... 2020-06-21T11:32:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:33:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:33:22 prefetch.2.10.7: 'SRR7506489' is valid 2020-06-21T11:33:22 prefetch.2.10.7: 1) 'SRR7506489' was downloaded successfully Read 8288774 spots for SRR7506489/SRR7506489.sra Written 8288774 spots for SRR7506489/SRR7506489.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: 00:01:07 8288774 reads; of these: 8288774 (100.00%) were unpaired; of these: 5626266 (67.88%) aligned 0 times 2085100 (25.16%) aligned exactly 1 time 577408 (6.97%) aligned >1 times 32.12% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 464005 / 2662508 = 0.1743 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 20:36:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.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 20:36:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:32: 1000000 INFO @ Sun, 21 Jun 2020 20:36:37: 2000000 INFO @ Sun, 21 Jun 2020 20:36:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:36:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:36:39: #1 total tags in treatment: 2198503 INFO @ Sun, 21 Jun 2020 20:36:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:39: #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 20:36:39: #1 tags after filtering in treatment: 2198166 INFO @ Sun, 21 Jun 2020 20:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:39: #2 number of paired peaks: 3063 INFO @ Sun, 21 Jun 2020 20:36:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:39: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 20:36:39: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 20:36:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.05_model.r INFO @ Sun, 21 Jun 2020 20:36:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.05_summits.bed INFO @ Sun, 21 Jun 2020 20:36:48: Done! pass1 - making usageList (204 chroms): 1 millis pass2 - checking and writing primary data (3832 records, 4 fields): 16 millis CompletedMACS2peakCalling 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 20:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.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 20:36:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:02: 1000000 INFO @ Sun, 21 Jun 2020 20:37:08: 2000000 INFO @ Sun, 21 Jun 2020 20:37:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:37:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:37:09: #1 total tags in treatment: 2198503 INFO @ Sun, 21 Jun 2020 20:37:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:09: #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 20:37:09: #1 tags after filtering in treatment: 2198166 INFO @ Sun, 21 Jun 2020 20:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:09: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:10: #2 number of paired peaks: 3063 INFO @ Sun, 21 Jun 2020 20:37:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:10: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 20:37:10: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 20:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.10_model.r INFO @ Sun, 21 Jun 2020 20:37:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.10_summits.bed INFO @ Sun, 21 Jun 2020 20:37:18: Done! pass1 - making usageList (99 chroms): 1 millis pass2 - checking and writing primary data (2669 records, 4 fields): 10 millis CompletedMACS2peakCalling 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 20:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.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 20:37:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:32: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:37:38: 2000000 INFO @ Sun, 21 Jun 2020 20:37:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:37:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:37:39: #1 total tags in treatment: 2198503 INFO @ Sun, 21 Jun 2020 20:37:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:39: #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 20:37:39: #1 tags after filtering in treatment: 2198166 INFO @ Sun, 21 Jun 2020 20:37:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:40: #2 number of paired peaks: 3063 INFO @ Sun, 21 Jun 2020 20:37:40: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:40: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:40: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:40: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:40: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 20:37:40: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 20:37:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.20_model.r INFO @ Sun, 21 Jun 2020 20:37:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:37:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375835/SRX4375835.20_summits.bed INFO @ Sun, 21 Jun 2020 20:37:48: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (1691 records, 4 fields): 7 millis CompletedMACS2peakCalling