Job ID = 6456136 SRX = SRX319056 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:37:44 prefetch.2.10.7: 1) Downloading 'SRR927433'... 2020-06-21T10:37:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:42:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:42:20 prefetch.2.10.7: 1) 'SRR927433' was downloaded successfully Read 37701690 spots for SRR927433/SRR927433.sra Written 37701690 spots for SRR927433/SRR927433.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: 00:05:21 37701690 reads; of these: 37701690 (100.00%) were unpaired; of these: 15664670 (41.55%) aligned 0 times 19230681 (51.01%) aligned exactly 1 time 2806339 (7.44%) aligned >1 times 58.45% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 7204013 / 22037020 = 0.3269 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 19:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.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 19:54:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:16: 1000000 INFO @ Sun, 21 Jun 2020 19:54:21: 2000000 INFO @ Sun, 21 Jun 2020 19:54:26: 3000000 INFO @ Sun, 21 Jun 2020 19:54:31: 4000000 INFO @ Sun, 21 Jun 2020 19:54:36: 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 19:54:41: 6000000 INFO @ Sun, 21 Jun 2020 19:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.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 19:54:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:46: 7000000 INFO @ Sun, 21 Jun 2020 19:54:47: 1000000 INFO @ Sun, 21 Jun 2020 19:54:51: 8000000 INFO @ Sun, 21 Jun 2020 19:54:53: 2000000 INFO @ Sun, 21 Jun 2020 19:54:56: 9000000 INFO @ Sun, 21 Jun 2020 19:54:58: 3000000 INFO @ Sun, 21 Jun 2020 19:55:01: 10000000 INFO @ Sun, 21 Jun 2020 19:55:03: 4000000 INFO @ Sun, 21 Jun 2020 19:55:06: 11000000 INFO @ Sun, 21 Jun 2020 19:55:08: 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 19:55:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.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 19:55:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:12: 12000000 INFO @ Sun, 21 Jun 2020 19:55:13: 6000000 INFO @ Sun, 21 Jun 2020 19:55:17: 1000000 INFO @ Sun, 21 Jun 2020 19:55:17: 13000000 INFO @ Sun, 21 Jun 2020 19:55:19: 7000000 INFO @ Sun, 21 Jun 2020 19:55:22: 2000000 INFO @ Sun, 21 Jun 2020 19:55:23: 14000000 INFO @ Sun, 21 Jun 2020 19:55:24: 8000000 INFO @ Sun, 21 Jun 2020 19:55:27: 3000000 INFO @ Sun, 21 Jun 2020 19:55:27: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:55:27: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:55:27: #1 total tags in treatment: 14833007 INFO @ Sun, 21 Jun 2020 19:55:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:27: #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 19:55:28: #1 tags after filtering in treatment: 14832977 INFO @ Sun, 21 Jun 2020 19:55:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:29: #2 number of paired peaks: 337 WARNING @ Sun, 21 Jun 2020 19:55:29: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Sun, 21 Jun 2020 19:55:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:29: #2 predicted fragment length is 267 bps INFO @ Sun, 21 Jun 2020 19:55:29: #2 alternative fragment length(s) may be 267 bps INFO @ Sun, 21 Jun 2020 19:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.05_model.r INFO @ Sun, 21 Jun 2020 19:55:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:29: 9000000 INFO @ Sun, 21 Jun 2020 19:55:32: 4000000 INFO @ Sun, 21 Jun 2020 19:55:34: 10000000 INFO @ Sun, 21 Jun 2020 19:55:37: 5000000 INFO @ Sun, 21 Jun 2020 19:55:39: 11000000 INFO @ Sun, 21 Jun 2020 19:55:42: 6000000 INFO @ Sun, 21 Jun 2020 19:55:44: 12000000 INFO @ Sun, 21 Jun 2020 19:55:47: 7000000 INFO @ Sun, 21 Jun 2020 19:55:50: 13000000 INFO @ Sun, 21 Jun 2020 19:55:53: 8000000 INFO @ Sun, 21 Jun 2020 19:55:56: 14000000 INFO @ Sun, 21 Jun 2020 19:55:59: 9000000 INFO @ Sun, 21 Jun 2020 19:56:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:56:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:56:00: #1 total tags in treatment: 14833007 INFO @ Sun, 21 Jun 2020 19:56:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:00: #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 19:56:01: #1 tags after filtering in treatment: 14832977 INFO @ Sun, 21 Jun 2020 19:56:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:02: #2 number of paired peaks: 337 WARNING @ Sun, 21 Jun 2020 19:56:02: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Sun, 21 Jun 2020 19:56:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:02: #2 predicted fragment length is 267 bps INFO @ Sun, 21 Jun 2020 19:56:02: #2 alternative fragment length(s) may be 267 bps INFO @ Sun, 21 Jun 2020 19:56:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.10_model.r INFO @ Sun, 21 Jun 2020 19:56:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:04: 10000000 INFO @ Sun, 21 Jun 2020 19:56:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:09: 11000000 INFO @ Sun, 21 Jun 2020 19:56:14: 12000000 INFO @ Sun, 21 Jun 2020 19:56:19: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:56:24: 14000000 INFO @ Sun, 21 Jun 2020 19:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.05_summits.bed INFO @ Sun, 21 Jun 2020 19:56:28: Done! INFO @ Sun, 21 Jun 2020 19:56:28: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:56:28: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:56:28: #1 total tags in treatment: 14833007 INFO @ Sun, 21 Jun 2020 19:56:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:28: #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 19:56:29: #1 tags after filtering in treatment: 14832977 INFO @ Sun, 21 Jun 2020 19:56:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:30: #2 number of paired peaks: 337 WARNING @ Sun, 21 Jun 2020 19:56:30: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Sun, 21 Jun 2020 19:56:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:30: #2 predicted fragment length is 267 bps INFO @ Sun, 21 Jun 2020 19:56:30: #2 alternative fragment length(s) may be 267 bps INFO @ Sun, 21 Jun 2020 19:56:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.20_model.r INFO @ Sun, 21 Jun 2020 19:56:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:30: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (313 chroms): 3 millis pass2 - checking and writing primary data (13886 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:56:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.10_summits.bed INFO @ Sun, 21 Jun 2020 19:56:56: Done! pass1 - making usageList (233 chroms): 2 millis pass2 - checking and writing primary data (7110 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:57:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX319056/SRX319056.20_summits.bed INFO @ Sun, 21 Jun 2020 19:57:25: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (2967 records, 4 fields): 8 millis CompletedMACS2peakCalling