Job ID = 6456518 SRX = SRX359797 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:31 prefetch.2.10.7: 1) Downloading 'SRR1002329'... 2020-06-21T10:52:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:39 prefetch.2.10.7: 1) 'SRR1002329' was downloaded successfully Read 21228362 spots for SRR1002329/SRR1002329.sra Written 21228362 spots for SRR1002329/SRR1002329.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: 00:04:49 21228362 reads; of these: 21228362 (100.00%) were unpaired; of these: 2612798 (12.31%) aligned 0 times 14079122 (66.32%) aligned exactly 1 time 4536442 (21.37%) aligned >1 times 87.69% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 4239571 / 18615564 = 0.2277 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 20:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.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 20:08:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:09: 1000000 INFO @ Sun, 21 Jun 2020 20:08:14: 2000000 INFO @ Sun, 21 Jun 2020 20:08:19: 3000000 INFO @ Sun, 21 Jun 2020 20:08:24: 4000000 INFO @ Sun, 21 Jun 2020 20:08:30: 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 20:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.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 20:08:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:35: 6000000 INFO @ Sun, 21 Jun 2020 20:08:40: 1000000 INFO @ Sun, 21 Jun 2020 20:08:42: 7000000 INFO @ Sun, 21 Jun 2020 20:08:46: 2000000 INFO @ Sun, 21 Jun 2020 20:08:48: 8000000 INFO @ Sun, 21 Jun 2020 20:08:53: 3000000 INFO @ Sun, 21 Jun 2020 20:08:54: 9000000 INFO @ Sun, 21 Jun 2020 20:08:59: 4000000 INFO @ Sun, 21 Jun 2020 20:09:00: 10000000 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 20:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.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 20:09:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:05: 5000000 INFO @ Sun, 21 Jun 2020 20:09:07: 11000000 INFO @ Sun, 21 Jun 2020 20:09:10: 1000000 INFO @ Sun, 21 Jun 2020 20:09:12: 6000000 INFO @ Sun, 21 Jun 2020 20:09:13: 12000000 INFO @ Sun, 21 Jun 2020 20:09:17: 2000000 INFO @ Sun, 21 Jun 2020 20:09:18: 7000000 INFO @ Sun, 21 Jun 2020 20:09:20: 13000000 INFO @ Sun, 21 Jun 2020 20:09:24: 3000000 INFO @ Sun, 21 Jun 2020 20:09:25: 8000000 INFO @ Sun, 21 Jun 2020 20:09:26: 14000000 INFO @ Sun, 21 Jun 2020 20:09:29: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 20:09:29: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 20:09:29: #1 total tags in treatment: 14375993 INFO @ Sun, 21 Jun 2020 20:09:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:29: #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 20:09:29: #1 tags after filtering in treatment: 14375920 INFO @ Sun, 21 Jun 2020 20:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:29: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:30: #2 number of paired peaks: 958 WARNING @ Sun, 21 Jun 2020 20:09:30: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sun, 21 Jun 2020 20:09:30: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:30: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:30: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:30: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:30: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 20:09:30: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sun, 21 Jun 2020 20:09:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.05_model.r INFO @ Sun, 21 Jun 2020 20:09:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:31: 4000000 INFO @ Sun, 21 Jun 2020 20:09:31: 9000000 INFO @ Sun, 21 Jun 2020 20:09:37: 10000000 INFO @ Sun, 21 Jun 2020 20:09:37: 5000000 INFO @ Sun, 21 Jun 2020 20:09:43: 11000000 INFO @ Sun, 21 Jun 2020 20:09:44: 6000000 INFO @ Sun, 21 Jun 2020 20:09:50: 12000000 INFO @ Sun, 21 Jun 2020 20:09:51: 7000000 INFO @ Sun, 21 Jun 2020 20:09:57: 13000000 INFO @ Sun, 21 Jun 2020 20:09:58: 8000000 INFO @ Sun, 21 Jun 2020 20:10:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:03: 14000000 INFO @ Sun, 21 Jun 2020 20:10:05: 9000000 INFO @ Sun, 21 Jun 2020 20:10:06: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 20:10:06: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 20:10:06: #1 total tags in treatment: 14375993 INFO @ Sun, 21 Jun 2020 20:10:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:10:06: #1 tags after filtering in treatment: 14375920 INFO @ Sun, 21 Jun 2020 20:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:07: #2 number of paired peaks: 958 WARNING @ Sun, 21 Jun 2020 20:10:07: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sun, 21 Jun 2020 20:10:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:07: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 20:10:07: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sun, 21 Jun 2020 20:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.10_model.r INFO @ Sun, 21 Jun 2020 20:10:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:11: 10000000 INFO @ Sun, 21 Jun 2020 20:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.05_summits.bed INFO @ Sun, 21 Jun 2020 20:10:16: Done! pass1 - making usageList (611 chroms): 2 millis pass2 - checking and writing primary data (4625 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:18: 11000000 INFO @ Sun, 21 Jun 2020 20:10:24: 12000000 INFO @ Sun, 21 Jun 2020 20:10:30: 13000000 INFO @ Sun, 21 Jun 2020 20:10:36: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:10:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:39: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 20:10:39: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 20:10:39: #1 total tags in treatment: 14375993 INFO @ Sun, 21 Jun 2020 20:10:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:39: #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 20:10:39: #1 tags after filtering in treatment: 14375920 INFO @ Sun, 21 Jun 2020 20:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:40: #2 number of paired peaks: 958 WARNING @ Sun, 21 Jun 2020 20:10:40: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sun, 21 Jun 2020 20:10:40: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:41: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 20:10:41: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sun, 21 Jun 2020 20:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.20_model.r INFO @ Sun, 21 Jun 2020 20:10:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.10_summits.bed INFO @ Sun, 21 Jun 2020 20:10:52: Done! pass1 - making usageList (453 chroms): 1 millis pass2 - checking and writing primary data (2414 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX359797/SRX359797.20_summits.bed INFO @ Sun, 21 Jun 2020 20:11:25: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (1002 records, 4 fields): 9 millis CompletedMACS2peakCalling