Job ID = 6452495 SRX = SRX013099 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:36 prefetch.2.10.7: 1) Downloading 'SRR030365'... 2020-06-21T07:38:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:40:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:40:02 prefetch.2.10.7: 'SRR030365' is valid 2020-06-21T07:40:02 prefetch.2.10.7: 1) 'SRR030365' was downloaded successfully Read 7652899 spots for SRR030365/SRR030365.sra Written 7652899 spots for SRR030365/SRR030365.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: 00:02:02 7652899 reads; of these: 7652899 (100.00%) were unpaired; of these: 275137 (3.60%) aligned 0 times 3846976 (50.27%) aligned exactly 1 time 3530786 (46.14%) aligned >1 times 96.40% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 948260 / 7377762 = 0.1285 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 16:44:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.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 16:44:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:27: 1000000 INFO @ Sun, 21 Jun 2020 16:44:33: 2000000 INFO @ Sun, 21 Jun 2020 16:44:39: 3000000 INFO @ Sun, 21 Jun 2020 16:44:44: 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 16:44:51: 5000000 INFO @ Sun, 21 Jun 2020 16:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.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 16:44:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:56: 1000000 INFO @ Sun, 21 Jun 2020 16:44:57: 6000000 INFO @ Sun, 21 Jun 2020 16:45:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:00: #1 total tags in treatment: 6429502 INFO @ Sun, 21 Jun 2020 16:45:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:00: #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 16:45:00: #1 tags after filtering in treatment: 6429486 INFO @ Sun, 21 Jun 2020 16:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:00: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:01: #2 number of paired peaks: 2699 INFO @ Sun, 21 Jun 2020 16:45:01: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:01: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:01: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:01: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:01: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 16:45:01: #2 alternative fragment length(s) may be 4,92,596,598 bps INFO @ Sun, 21 Jun 2020 16:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.05_model.r INFO @ Sun, 21 Jun 2020 16:45:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:02: 2000000 INFO @ Sun, 21 Jun 2020 16:45:07: 3000000 INFO @ Sun, 21 Jun 2020 16:45:12: 4000000 INFO @ Sun, 21 Jun 2020 16:45:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:18: 5000000 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 16:45:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.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 16:45:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:45:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:45:23: 6000000 INFO @ Sun, 21 Jun 2020 16:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.05_summits.bed INFO @ Sun, 21 Jun 2020 16:45:24: Done! pass1 - making usageList (922 chroms): 1 millis pass2 - checking and writing primary data (4498 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:45:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:25: #1 total tags in treatment: 6429502 INFO @ Sun, 21 Jun 2020 16:45:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:25: #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 16:45:25: #1 tags after filtering in treatment: 6429486 INFO @ Sun, 21 Jun 2020 16:45:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:25: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:26: #2 number of paired peaks: 2699 INFO @ Sun, 21 Jun 2020 16:45:26: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:26: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:26: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:26: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:26: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 16:45:26: #2 alternative fragment length(s) may be 4,92,596,598 bps INFO @ Sun, 21 Jun 2020 16:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.10_model.r INFO @ Sun, 21 Jun 2020 16:45:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:26: 1000000 INFO @ Sun, 21 Jun 2020 16:45:31: 2000000 INFO @ Sun, 21 Jun 2020 16:45:36: 3000000 INFO @ Sun, 21 Jun 2020 16:45:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:41: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:45:47: 5000000 INFO @ Sun, 21 Jun 2020 16:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.10_summits.bed INFO @ Sun, 21 Jun 2020 16:45:47: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (1685 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:45:52: 6000000 INFO @ Sun, 21 Jun 2020 16:45:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:54: #1 total tags in treatment: 6429502 INFO @ Sun, 21 Jun 2020 16:45:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:54: #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 16:45:54: #1 tags after filtering in treatment: 6429486 INFO @ Sun, 21 Jun 2020 16:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:54: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:55: #2 number of paired peaks: 2699 INFO @ Sun, 21 Jun 2020 16:45:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:55: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:55: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:55: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:55: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 16:45:55: #2 alternative fragment length(s) may be 4,92,596,598 bps INFO @ Sun, 21 Jun 2020 16:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.20_model.r INFO @ Sun, 21 Jun 2020 16:45:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:46:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013099/SRX013099.20_summits.bed INFO @ Sun, 21 Jun 2020 16:46:16: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 12 millis CompletedMACS2peakCalling