Job ID = 6452402 SRX = SRX013036 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:08 prefetch.2.10.7: 1) Downloading 'SRR030302'... 2020-06-21T07:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:00:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:00:06 prefetch.2.10.7: 'SRR030302' is valid 2020-06-21T08:00:06 prefetch.2.10.7: 1) 'SRR030302' was downloaded successfully Read 3824343 spots for SRR030302/SRR030302.sra Written 3824343 spots for SRR030302/SRR030302.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: 00:00:30 3824343 reads; of these: 3824343 (100.00%) were unpaired; of these: 1245248 (32.56%) aligned 0 times 2326433 (60.83%) aligned exactly 1 time 252662 (6.61%) aligned >1 times 67.44% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 110715 / 2579095 = 0.0429 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 17:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.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 17:01:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:01:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:01:58: 1000000 INFO @ Sun, 21 Jun 2020 17:02:03: 2000000 INFO @ Sun, 21 Jun 2020 17:02:06: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:02:06: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:02:06: #1 total tags in treatment: 2468380 INFO @ Sun, 21 Jun 2020 17:02:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:02:06: #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 17:02:06: #1 tags after filtering in treatment: 2467996 INFO @ Sun, 21 Jun 2020 17:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:02:06: #1 finished! INFO @ Sun, 21 Jun 2020 17:02:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:02:06: #2 number of paired peaks: 1502 INFO @ Sun, 21 Jun 2020 17:02:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:02:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:02:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:02:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:02:06: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 17:02:06: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 17:02:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.05_model.r INFO @ Sun, 21 Jun 2020 17:02:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:02:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:02:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.05_summits.bed INFO @ Sun, 21 Jun 2020 17:02:16: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (2608 records, 4 fields): 5 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 17:02:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.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 17:02:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:02:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:02:28: 1000000 INFO @ Sun, 21 Jun 2020 17:02:33: 2000000 INFO @ Sun, 21 Jun 2020 17:02:36: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:02:36: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:02:36: #1 total tags in treatment: 2468380 INFO @ Sun, 21 Jun 2020 17:02:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:02:36: #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 17:02:36: #1 tags after filtering in treatment: 2467996 INFO @ Sun, 21 Jun 2020 17:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:02:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:02:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:02:37: #2 number of paired peaks: 1502 INFO @ Sun, 21 Jun 2020 17:02:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:02:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:02:37: end of X-cor INFO @ Sun, 21 Jun 2020 17:02:37: #2 finished! INFO @ Sun, 21 Jun 2020 17:02:37: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 17:02:37: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 17:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.10_model.r INFO @ Sun, 21 Jun 2020 17:02:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:02:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:02:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:02:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:02:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.10_summits.bed INFO @ Sun, 21 Jun 2020 17:02:46: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (891 records, 4 fields): 3 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 17:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.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 17:02:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:02:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:02:59: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:03:04: 2000000 INFO @ Sun, 21 Jun 2020 17:03:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:03:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:03:08: #1 total tags in treatment: 2468380 INFO @ Sun, 21 Jun 2020 17:03:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:03:08: #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 17:03:08: #1 tags after filtering in treatment: 2467996 INFO @ Sun, 21 Jun 2020 17:03:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:03:08: #1 finished! INFO @ Sun, 21 Jun 2020 17:03:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:03:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:03:08: #2 number of paired peaks: 1502 INFO @ Sun, 21 Jun 2020 17:03:08: start model_add_line... INFO @ Sun, 21 Jun 2020 17:03:08: start X-correlation... INFO @ Sun, 21 Jun 2020 17:03:08: end of X-cor INFO @ Sun, 21 Jun 2020 17:03:08: #2 finished! INFO @ Sun, 21 Jun 2020 17:03:08: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 17:03:08: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 17:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.20_model.r INFO @ Sun, 21 Jun 2020 17:03:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:03:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:03:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013036/SRX013036.20_summits.bed INFO @ Sun, 21 Jun 2020 17:03:17: Done! pass1 - making usageList (20 chroms): 2 millis pass2 - checking and writing primary data (134 records, 4 fields): 2 millis CompletedMACS2peakCalling