Job ID = 6452379 SRX = SRX013019 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:24:17 prefetch.2.10.7: 1) Downloading 'SRR030285'... 2020-06-21T07:24:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:25:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:25:26 prefetch.2.10.7: 'SRR030285' is valid 2020-06-21T07:25:26 prefetch.2.10.7: 1) 'SRR030285' was downloaded successfully Read 6402844 spots for SRR030285/SRR030285.sra Written 6402844 spots for SRR030285/SRR030285.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: 00:01:02 6402844 reads; of these: 6402844 (100.00%) were unpaired; of these: 694099 (10.84%) aligned 0 times 5042700 (78.76%) aligned exactly 1 time 666045 (10.40%) aligned >1 times 89.16% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 492937 / 5708745 = 0.0863 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 16:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.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 16:28:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:28:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:28:31: 1000000 INFO @ Sun, 21 Jun 2020 16:28:37: 2000000 INFO @ Sun, 21 Jun 2020 16:28:42: 3000000 INFO @ Sun, 21 Jun 2020 16:28:47: 4000000 INFO @ Sun, 21 Jun 2020 16:28:53: 5000000 INFO @ Sun, 21 Jun 2020 16:28:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:28:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:28:54: #1 total tags in treatment: 5215808 INFO @ Sun, 21 Jun 2020 16:28:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:28:54: #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 16:28:54: #1 tags after filtering in treatment: 5215581 INFO @ Sun, 21 Jun 2020 16:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:28:54: #1 finished! INFO @ Sun, 21 Jun 2020 16:28:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:28:54: #2 looking for paired plus/minus strand peaks... 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 16:28:55: #2 number of paired peaks: 5420 INFO @ Sun, 21 Jun 2020 16:28:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:28:55: start X-correlation... INFO @ Sun, 21 Jun 2020 16:28:55: end of X-cor INFO @ Sun, 21 Jun 2020 16:28:55: #2 finished! INFO @ Sun, 21 Jun 2020 16:28:55: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 16:28:55: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 16:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.05_model.r INFO @ Sun, 21 Jun 2020 16:28:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.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 16:28:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:28:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:29:01: 1000000 INFO @ Sun, 21 Jun 2020 16:29:07: 2000000 INFO @ Sun, 21 Jun 2020 16:29:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:29:12: 3000000 INFO @ Sun, 21 Jun 2020 16:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.05_summits.bed INFO @ Sun, 21 Jun 2020 16:29:14: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (7792 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:29:17: 4000000 INFO @ Sun, 21 Jun 2020 16:29:23: 5000000 INFO @ Sun, 21 Jun 2020 16:29:24: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:29:24: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:29:24: #1 total tags in treatment: 5215808 INFO @ Sun, 21 Jun 2020 16:29:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:29:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 16:29:24: #1 tags after filtering in treatment: 5215581 INFO @ Sun, 21 Jun 2020 16:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:29:24: #1 finished! INFO @ Sun, 21 Jun 2020 16:29:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:29:25: #2 number of paired peaks: 5420 INFO @ Sun, 21 Jun 2020 16:29:25: start model_add_line... INFO @ Sun, 21 Jun 2020 16:29:25: start X-correlation... INFO @ Sun, 21 Jun 2020 16:29:25: end of X-cor INFO @ Sun, 21 Jun 2020 16:29:25: #2 finished! INFO @ Sun, 21 Jun 2020 16:29:25: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 16:29:25: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 16:29:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.10_model.r INFO @ Sun, 21 Jun 2020 16:29:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:29:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.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 16:29:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:29:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:29:33: 1000000 INFO @ Sun, 21 Jun 2020 16:29:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:29:39: 2000000 INFO @ Sun, 21 Jun 2020 16:29:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:29:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:29:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.10_summits.bed INFO @ Sun, 21 Jun 2020 16:29:44: Done! pass1 - making usageList (101 chroms): 2 millis pass2 - checking and writing primary data (5356 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:29:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:29:51: 4000000 INFO @ Sun, 21 Jun 2020 16:29:58: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:30:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:30:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:30:00: #1 total tags in treatment: 5215808 INFO @ Sun, 21 Jun 2020 16:30:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:30:00: #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 16:30:00: #1 tags after filtering in treatment: 5215581 INFO @ Sun, 21 Jun 2020 16:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:30:00: #1 finished! INFO @ Sun, 21 Jun 2020 16:30:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:30:01: #2 number of paired peaks: 5420 INFO @ Sun, 21 Jun 2020 16:30:01: start model_add_line... INFO @ Sun, 21 Jun 2020 16:30:01: start X-correlation... INFO @ Sun, 21 Jun 2020 16:30:01: end of X-cor INFO @ Sun, 21 Jun 2020 16:30:01: #2 finished! INFO @ Sun, 21 Jun 2020 16:30:01: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 16:30:01: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 16:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.20_model.r INFO @ Sun, 21 Jun 2020 16:30:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:30:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:30:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013019/SRX013019.20_summits.bed INFO @ Sun, 21 Jun 2020 16:30:19: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (3207 records, 4 fields): 7 millis CompletedMACS2peakCalling