Job ID = 6454078 SRX = SRX181424 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:24 prefetch.2.10.7: 1) Downloading 'SRR548161'... 2020-06-21T09:06:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:09:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:09:54 prefetch.2.10.7: 1) 'SRR548161' was downloaded successfully Read 26791329 spots for SRR548161/SRR548161.sra Written 26791329 spots for SRR548161/SRR548161.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: 00:04:06 26791329 reads; of these: 26791329 (100.00%) were unpaired; of these: 4836138 (18.05%) aligned 0 times 20191023 (75.36%) aligned exactly 1 time 1764168 (6.58%) aligned >1 times 81.95% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 16556127 / 21955191 = 0.7541 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 18:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.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 18:18:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:33: 1000000 INFO @ Sun, 21 Jun 2020 18:18:37: 2000000 INFO @ Sun, 21 Jun 2020 18:18:42: 3000000 INFO @ Sun, 21 Jun 2020 18:18:47: 4000000 INFO @ Sun, 21 Jun 2020 18:18:52: 5000000 INFO @ Sun, 21 Jun 2020 18:18:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:18:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:18:54: #1 total tags in treatment: 5399064 INFO @ Sun, 21 Jun 2020 18:18:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:54: #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 18:18:55: #1 tags after filtering in treatment: 5398952 INFO @ Sun, 21 Jun 2020 18:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:55: #2 number of paired peaks: 1372 INFO @ Sun, 21 Jun 2020 18:18:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:55: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 18:18:55: #2 alternative fragment length(s) may be 137,160 bps INFO @ Sun, 21 Jun 2020 18:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.05_model.r INFO @ Sun, 21 Jun 2020 18:18:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:55: #3 Pre-compute pvalue-qvalue table... 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 18:18:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.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 18:18:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:04: 1000000 INFO @ Sun, 21 Jun 2020 18:19:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:09: 2000000 INFO @ Sun, 21 Jun 2020 18:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.05_summits.bed INFO @ Sun, 21 Jun 2020 18:19:13: Done! INFO @ Sun, 21 Jun 2020 18:19:15: 3000000 pass1 - making usageList (251 chroms): 1 millis pass2 - checking and writing primary data (3735 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:19:20: 4000000 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 18:19:27: 5000000 INFO @ Sun, 21 Jun 2020 18:19:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.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 18:19:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:19:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:19:29: #1 total tags in treatment: 5399064 INFO @ Sun, 21 Jun 2020 18:19:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:29: #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 18:19:29: #1 tags after filtering in treatment: 5398952 INFO @ Sun, 21 Jun 2020 18:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:30: #2 number of paired peaks: 1372 INFO @ Sun, 21 Jun 2020 18:19:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:30: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 18:19:30: #2 alternative fragment length(s) may be 137,160 bps INFO @ Sun, 21 Jun 2020 18:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.10_model.r INFO @ Sun, 21 Jun 2020 18:19:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:34: 1000000 INFO @ Sun, 21 Jun 2020 18:19:40: 2000000 INFO @ Sun, 21 Jun 2020 18:19:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:46: 3000000 INFO @ Sun, 21 Jun 2020 18:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.10_summits.bed INFO @ Sun, 21 Jun 2020 18:19:48: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (835 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:19:51: 4000000 INFO @ Sun, 21 Jun 2020 18:19:58: 5000000 INFO @ Sun, 21 Jun 2020 18:20:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:20:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:20:00: #1 total tags in treatment: 5399064 INFO @ Sun, 21 Jun 2020 18:20:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:00: #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 18:20:01: #1 tags after filtering in treatment: 5398952 INFO @ Sun, 21 Jun 2020 18:20:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:01: #2 number of paired peaks: 1372 INFO @ Sun, 21 Jun 2020 18:20:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:01: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 18:20:01: #2 alternative fragment length(s) may be 137,160 bps INFO @ Sun, 21 Jun 2020 18:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.20_model.r INFO @ Sun, 21 Jun 2020 18:20:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:20:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181424/SRX181424.20_summits.bed INFO @ Sun, 21 Jun 2020 18:20:19: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 3 millis CompletedMACS2peakCalling