Job ID = 6456227 SRX = SRX331383 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:37:14 prefetch.2.10.7: 1) Downloading 'SRR947620'... 2020-06-21T10:37:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:08 prefetch.2.10.7: 1) 'SRR947620' was downloaded successfully Read 17517323 spots for SRR947620/SRR947620.sra Written 17517323 spots for SRR947620/SRR947620.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: 00:03:39 17517323 reads; of these: 17517323 (100.00%) were unpaired; of these: 964170 (5.50%) aligned 0 times 15765699 (90.00%) aligned exactly 1 time 787454 (4.50%) aligned >1 times 94.50% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6310730 / 16553153 = 0.3812 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 19:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.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 19:49:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:40: 1000000 INFO @ Sun, 21 Jun 2020 19:49:45: 2000000 INFO @ Sun, 21 Jun 2020 19:49:51: 3000000 INFO @ Sun, 21 Jun 2020 19:49:56: 4000000 INFO @ Sun, 21 Jun 2020 19:50:01: 5000000 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 19:50:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.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 19:50:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:07: 6000000 INFO @ Sun, 21 Jun 2020 19:50:09: 1000000 INFO @ Sun, 21 Jun 2020 19:50:12: 7000000 INFO @ Sun, 21 Jun 2020 19:50:15: 2000000 INFO @ Sun, 21 Jun 2020 19:50:18: 8000000 INFO @ Sun, 21 Jun 2020 19:50:20: 3000000 INFO @ Sun, 21 Jun 2020 19:50:24: 9000000 INFO @ Sun, 21 Jun 2020 19:50:25: 4000000 INFO @ Sun, 21 Jun 2020 19:50:29: 10000000 INFO @ Sun, 21 Jun 2020 19:50:30: 5000000 INFO @ Sun, 21 Jun 2020 19:50:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:31: #1 total tags in treatment: 10242423 INFO @ Sun, 21 Jun 2020 19:50:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:31: #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 19:50:32: #1 tags after filtering in treatment: 10242133 INFO @ Sun, 21 Jun 2020 19:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:32: #2 looking for paired plus/minus strand peaks... 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 19:50:33: #2 number of paired peaks: 12502 INFO @ Sun, 21 Jun 2020 19:50:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:33: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 19:50:33: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 19:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.05_model.r INFO @ Sun, 21 Jun 2020 19:50:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.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 19:50:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:35: 6000000 INFO @ Sun, 21 Jun 2020 19:50:39: 1000000 INFO @ Sun, 21 Jun 2020 19:50:40: 7000000 INFO @ Sun, 21 Jun 2020 19:50:44: 2000000 INFO @ Sun, 21 Jun 2020 19:50:45: 8000000 INFO @ Sun, 21 Jun 2020 19:50:50: 3000000 INFO @ Sun, 21 Jun 2020 19:50:51: 9000000 INFO @ Sun, 21 Jun 2020 19:50:55: 4000000 INFO @ Sun, 21 Jun 2020 19:50:56: 10000000 INFO @ Sun, 21 Jun 2020 19:50:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:57: #1 total tags in treatment: 10242423 INFO @ Sun, 21 Jun 2020 19:50:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:57: #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 19:50:58: #1 tags after filtering in treatment: 10242133 INFO @ Sun, 21 Jun 2020 19:50:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:59: #2 number of paired peaks: 12502 INFO @ Sun, 21 Jun 2020 19:50:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:00: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 19:51:00: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 19:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.10_model.r INFO @ Sun, 21 Jun 2020 19:51:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:00: 5000000 INFO @ Sun, 21 Jun 2020 19:51:05: 6000000 INFO @ Sun, 21 Jun 2020 19:51:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:10: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:51:15: 8000000 INFO @ Sun, 21 Jun 2020 19:51:20: 9000000 INFO @ Sun, 21 Jun 2020 19:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.05_summits.bed INFO @ Sun, 21 Jun 2020 19:51:23: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (7181 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:25: 10000000 INFO @ Sun, 21 Jun 2020 19:51:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:27: #1 total tags in treatment: 10242423 INFO @ Sun, 21 Jun 2020 19:51:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:27: #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 19:51:27: #1 tags after filtering in treatment: 10242133 INFO @ Sun, 21 Jun 2020 19:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:27: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:29: #2 number of paired peaks: 12502 INFO @ Sun, 21 Jun 2020 19:51:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:29: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 19:51:29: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 19:51:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.20_model.r INFO @ Sun, 21 Jun 2020 19:51:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:51: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (6886 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331383/SRX331383.20_summits.bed INFO @ Sun, 21 Jun 2020 19:52:19: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (6504 records, 4 fields): 9 millis CompletedMACS2peakCalling