Job ID = 6453778 SRX = SRX147005 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:34:09 prefetch.2.10.7: 1) Downloading 'SRR495379'... 2020-06-21T08:34:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:52 prefetch.2.10.7: 'SRR495379' is valid 2020-06-21T08:36:52 prefetch.2.10.7: 1) 'SRR495379' was downloaded successfully Read 16320767 spots for SRR495379/SRR495379.sra Written 16320767 spots for SRR495379/SRR495379.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: 00:04:36 16320767 reads; of these: 16320767 (100.00%) were unpaired; of these: 339312 (2.08%) aligned 0 times 11319941 (69.36%) aligned exactly 1 time 4661514 (28.56%) aligned >1 times 97.92% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 2391095 / 15981455 = 0.1496 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 17:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.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 17:46:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:22: 1000000 INFO @ Sun, 21 Jun 2020 17:46:28: 2000000 INFO @ Sun, 21 Jun 2020 17:46:34: 3000000 INFO @ Sun, 21 Jun 2020 17:46:40: 4000000 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 17:46:45: 5000000 INFO @ Sun, 21 Jun 2020 17:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.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 17:46:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:51: 6000000 INFO @ Sun, 21 Jun 2020 17:46:52: 1000000 INFO @ Sun, 21 Jun 2020 17:46:56: 7000000 INFO @ Sun, 21 Jun 2020 17:46:58: 2000000 INFO @ Sun, 21 Jun 2020 17:47:02: 8000000 INFO @ Sun, 21 Jun 2020 17:47:03: 3000000 INFO @ Sun, 21 Jun 2020 17:47:07: 9000000 INFO @ Sun, 21 Jun 2020 17:47:09: 4000000 INFO @ Sun, 21 Jun 2020 17:47:12: 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 17:47:15: 5000000 INFO @ Sun, 21 Jun 2020 17:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.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 17:47:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:18: 11000000 INFO @ Sun, 21 Jun 2020 17:47:20: 6000000 INFO @ Sun, 21 Jun 2020 17:47:23: 1000000 INFO @ Sun, 21 Jun 2020 17:47:24: 12000000 INFO @ Sun, 21 Jun 2020 17:47:26: 7000000 INFO @ Sun, 21 Jun 2020 17:47:29: 2000000 INFO @ Sun, 21 Jun 2020 17:47:30: 13000000 INFO @ Sun, 21 Jun 2020 17:47:32: 8000000 INFO @ Sun, 21 Jun 2020 17:47:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:47:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:47:33: #1 total tags in treatment: 13590360 INFO @ Sun, 21 Jun 2020 17:47:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:33: #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 17:47:34: #1 tags after filtering in treatment: 13590217 INFO @ Sun, 21 Jun 2020 17:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:35: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 17:47:35: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 17:47:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:35: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 17:47:35: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 17:47:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.05_model.r INFO @ Sun, 21 Jun 2020 17:47:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:35: 3000000 INFO @ Sun, 21 Jun 2020 17:47:37: 9000000 INFO @ Sun, 21 Jun 2020 17:47:41: 4000000 INFO @ Sun, 21 Jun 2020 17:47:43: 10000000 INFO @ Sun, 21 Jun 2020 17:47:47: 5000000 INFO @ Sun, 21 Jun 2020 17:47:49: 11000000 INFO @ Sun, 21 Jun 2020 17:47:53: 6000000 INFO @ Sun, 21 Jun 2020 17:47:55: 12000000 INFO @ Sun, 21 Jun 2020 17:48:00: 7000000 INFO @ Sun, 21 Jun 2020 17:48:01: 13000000 INFO @ Sun, 21 Jun 2020 17:48:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:48:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:48:05: #1 total tags in treatment: 13590360 INFO @ Sun, 21 Jun 2020 17:48:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:05: #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 17:48:05: #1 tags after filtering in treatment: 13590217 INFO @ Sun, 21 Jun 2020 17:48:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:06: 8000000 INFO @ Sun, 21 Jun 2020 17:48:06: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 17:48:06: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:06: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 17:48:06: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 17:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.10_model.r INFO @ Sun, 21 Jun 2020 17:48:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:12: 9000000 INFO @ Sun, 21 Jun 2020 17:48:18: 10000000 INFO @ Sun, 21 Jun 2020 17:48:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.05_summits.bed INFO @ Sun, 21 Jun 2020 17:48:23: Done! pass1 - making usageList (514 chroms): 2 millis pass2 - checking and writing primary data (5787 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:48:24: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:48:31: 12000000 INFO @ Sun, 21 Jun 2020 17:48:37: 13000000 INFO @ Sun, 21 Jun 2020 17:48:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:48:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:48:41: #1 total tags in treatment: 13590360 INFO @ Sun, 21 Jun 2020 17:48:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:41: #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 17:48:42: #1 tags after filtering in treatment: 13590217 INFO @ Sun, 21 Jun 2020 17:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:43: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 17:48:43: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:43: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 17:48:43: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 17:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.20_model.r INFO @ Sun, 21 Jun 2020 17:48:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.10_summits.bed INFO @ Sun, 21 Jun 2020 17:48:55: Done! pass1 - making usageList (340 chroms): 1 millis pass2 - checking and writing primary data (1911 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX147005/SRX147005.20_summits.bed INFO @ Sun, 21 Jun 2020 17:49:30: Done! pass1 - making usageList (233 chroms): 0 millis pass2 - checking and writing primary data (759 records, 4 fields): 8 millis CompletedMACS2peakCalling