Job ID = 6453141 SRX = SRX104964 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:02:53 prefetch.2.10.7: 1) Downloading 'SRR363408'... 2020-06-21T08:02:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:07:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:07:22 prefetch.2.10.7: 1) 'SRR363408' was downloaded successfully Read 37480643 spots for SRR363408/SRR363408.sra Written 37480643 spots for SRR363408/SRR363408.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: 00:07:25 37480643 reads; of these: 37480643 (100.00%) were unpaired; of these: 3370132 (8.99%) aligned 0 times 29434135 (78.53%) aligned exactly 1 time 4676376 (12.48%) aligned >1 times 91.01% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 12 files... [bam_rmdupse_core] 9112291 / 34110511 = 0.2671 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 17:23:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.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 17:23:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:17: 1000000 INFO @ Sun, 21 Jun 2020 17:23:22: 2000000 INFO @ Sun, 21 Jun 2020 17:23:27: 3000000 INFO @ Sun, 21 Jun 2020 17:23:32: 4000000 INFO @ Sun, 21 Jun 2020 17:23:37: 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 17:23:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.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 17:23:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:42: 6000000 INFO @ Sun, 21 Jun 2020 17:23:47: 1000000 INFO @ Sun, 21 Jun 2020 17:23:48: 7000000 INFO @ Sun, 21 Jun 2020 17:23:52: 2000000 INFO @ Sun, 21 Jun 2020 17:23:53: 8000000 INFO @ Sun, 21 Jun 2020 17:23:57: 3000000 INFO @ Sun, 21 Jun 2020 17:23:58: 9000000 INFO @ Sun, 21 Jun 2020 17:24:03: 4000000 INFO @ Sun, 21 Jun 2020 17:24:03: 10000000 INFO @ Sun, 21 Jun 2020 17:24:08: 5000000 INFO @ Sun, 21 Jun 2020 17:24:09: 11000000 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 17:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.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 17:24:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:14: 6000000 INFO @ Sun, 21 Jun 2020 17:24:14: 12000000 INFO @ Sun, 21 Jun 2020 17:24:19: 1000000 INFO @ Sun, 21 Jun 2020 17:24:20: 7000000 INFO @ Sun, 21 Jun 2020 17:24:20: 13000000 INFO @ Sun, 21 Jun 2020 17:24:25: 8000000 INFO @ Sun, 21 Jun 2020 17:24:26: 2000000 INFO @ Sun, 21 Jun 2020 17:24:26: 14000000 INFO @ Sun, 21 Jun 2020 17:24:31: 9000000 INFO @ Sun, 21 Jun 2020 17:24:32: 15000000 INFO @ Sun, 21 Jun 2020 17:24:32: 3000000 INFO @ Sun, 21 Jun 2020 17:24:37: 10000000 INFO @ Sun, 21 Jun 2020 17:24:37: 16000000 INFO @ Sun, 21 Jun 2020 17:24:39: 4000000 INFO @ Sun, 21 Jun 2020 17:24:42: 11000000 INFO @ Sun, 21 Jun 2020 17:24:43: 17000000 INFO @ Sun, 21 Jun 2020 17:24:46: 5000000 INFO @ Sun, 21 Jun 2020 17:24:48: 12000000 INFO @ Sun, 21 Jun 2020 17:24:49: 18000000 INFO @ Sun, 21 Jun 2020 17:24:53: 6000000 INFO @ Sun, 21 Jun 2020 17:24:54: 13000000 INFO @ Sun, 21 Jun 2020 17:24:54: 19000000 INFO @ Sun, 21 Jun 2020 17:24:59: 7000000 INFO @ Sun, 21 Jun 2020 17:24:59: 14000000 INFO @ Sun, 21 Jun 2020 17:25:00: 20000000 INFO @ Sun, 21 Jun 2020 17:25:05: 15000000 INFO @ Sun, 21 Jun 2020 17:25:06: 8000000 INFO @ Sun, 21 Jun 2020 17:25:06: 21000000 INFO @ Sun, 21 Jun 2020 17:25:11: 16000000 INFO @ Sun, 21 Jun 2020 17:25:11: 22000000 INFO @ Sun, 21 Jun 2020 17:25:12: 9000000 INFO @ Sun, 21 Jun 2020 17:25:16: 17000000 INFO @ Sun, 21 Jun 2020 17:25:17: 23000000 INFO @ Sun, 21 Jun 2020 17:25:18: 10000000 INFO @ Sun, 21 Jun 2020 17:25:22: 18000000 INFO @ Sun, 21 Jun 2020 17:25:22: 24000000 INFO @ Sun, 21 Jun 2020 17:25:25: 11000000 INFO @ Sun, 21 Jun 2020 17:25:27: 19000000 INFO @ Sun, 21 Jun 2020 17:25:28: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:25:28: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:25:28: #1 total tags in treatment: 24998220 INFO @ Sun, 21 Jun 2020 17:25:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:28: #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 17:25:29: #1 tags after filtering in treatment: 24998212 INFO @ Sun, 21 Jun 2020 17:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:31: #2 number of paired peaks: 248 WARNING @ Sun, 21 Jun 2020 17:25:31: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 21 Jun 2020 17:25:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:31: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 17:25:31: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 21 Jun 2020 17:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.05_model.r INFO @ Sun, 21 Jun 2020 17:25:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:31: 12000000 INFO @ Sun, 21 Jun 2020 17:25:33: 20000000 INFO @ Sun, 21 Jun 2020 17:25:37: 13000000 INFO @ Sun, 21 Jun 2020 17:25:39: 21000000 INFO @ Sun, 21 Jun 2020 17:25:43: 14000000 INFO @ Sun, 21 Jun 2020 17:25:44: 22000000 INFO @ Sun, 21 Jun 2020 17:25:49: 23000000 INFO @ Sun, 21 Jun 2020 17:25:50: 15000000 INFO @ Sun, 21 Jun 2020 17:25:55: 24000000 INFO @ Sun, 21 Jun 2020 17:25:56: 16000000 INFO @ Sun, 21 Jun 2020 17:26:01: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:26:01: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:26:01: #1 total tags in treatment: 24998220 INFO @ Sun, 21 Jun 2020 17:26:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:01: #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 17:26:01: #1 tags after filtering in treatment: 24998212 INFO @ Sun, 21 Jun 2020 17:26:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:02: 17000000 INFO @ Sun, 21 Jun 2020 17:26:03: #2 number of paired peaks: 248 WARNING @ Sun, 21 Jun 2020 17:26:03: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 21 Jun 2020 17:26:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:03: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 17:26:03: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 21 Jun 2020 17:26:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.10_model.r INFO @ Sun, 21 Jun 2020 17:26:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:26:08: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:26:14: 19000000 INFO @ Sun, 21 Jun 2020 17:26:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:21: 20000000 INFO @ Sun, 21 Jun 2020 17:26:28: 21000000 INFO @ Sun, 21 Jun 2020 17:26:34: 22000000 INFO @ Sun, 21 Jun 2020 17:26:40: 23000000 INFO @ Sun, 21 Jun 2020 17:26:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.05_summits.bed INFO @ Sun, 21 Jun 2020 17:26:41: Done! pass1 - making usageList (250 chroms): 2 millis pass2 - checking and writing primary data (11353 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:46: 24000000 INFO @ Sun, 21 Jun 2020 17:26:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:52: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:26:52: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:26:52: #1 total tags in treatment: 24998220 INFO @ Sun, 21 Jun 2020 17:26:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:52: #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 17:26:52: #1 tags after filtering in treatment: 24998212 INFO @ Sun, 21 Jun 2020 17:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:54: #2 number of paired peaks: 248 WARNING @ Sun, 21 Jun 2020 17:26:54: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 21 Jun 2020 17:26:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:54: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 17:26:54: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 21 Jun 2020 17:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.20_model.r INFO @ Sun, 21 Jun 2020 17:26:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.10_summits.bed INFO @ Sun, 21 Jun 2020 17:27:15: Done! pass1 - making usageList (151 chroms): 1 millis pass2 - checking and writing primary data (4139 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:27:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104964/SRX104964.20_summits.bed INFO @ Sun, 21 Jun 2020 17:28:06: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (1473 records, 4 fields): 5 millis CompletedMACS2peakCalling