Job ID = 6452825 SRX = SRX041385 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:44:06 prefetch.2.10.7: 1) Downloading 'SRR099114'... 2020-06-21T07:44:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:45:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:45:47 prefetch.2.10.7: 'SRR099114' is valid 2020-06-21T07:45:47 prefetch.2.10.7: 1) 'SRR099114' was downloaded successfully Read 18243271 spots for SRR099114/SRR099114.sra Written 18243271 spots for SRR099114/SRR099114.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: 00:02:46 18243271 reads; of these: 18243271 (100.00%) were unpaired; of these: 848007 (4.65%) aligned 0 times 12433612 (68.15%) aligned exactly 1 time 4961652 (27.20%) aligned >1 times 95.35% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 3533577 / 17395264 = 0.2031 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 16:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.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 16:52:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:39: 1000000 INFO @ Sun, 21 Jun 2020 16:52:44: 2000000 INFO @ Sun, 21 Jun 2020 16:52:49: 3000000 INFO @ Sun, 21 Jun 2020 16:52:54: 4000000 INFO @ Sun, 21 Jun 2020 16:52:58: 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 16:53:03: 6000000 INFO @ Sun, 21 Jun 2020 16:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.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 16:53:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:08: 7000000 INFO @ Sun, 21 Jun 2020 16:53:09: 1000000 INFO @ Sun, 21 Jun 2020 16:53:13: 8000000 INFO @ Sun, 21 Jun 2020 16:53:13: 2000000 INFO @ Sun, 21 Jun 2020 16:53:17: 3000000 INFO @ Sun, 21 Jun 2020 16:53:17: 9000000 INFO @ Sun, 21 Jun 2020 16:53:21: 4000000 INFO @ Sun, 21 Jun 2020 16:53:22: 10000000 INFO @ Sun, 21 Jun 2020 16:53:26: 5000000 INFO @ Sun, 21 Jun 2020 16:53:27: 11000000 INFO @ Sun, 21 Jun 2020 16:53:30: 6000000 INFO @ Sun, 21 Jun 2020 16:53:32: 12000000 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 16:53:34: 7000000 INFO @ Sun, 21 Jun 2020 16:53:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.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 16:53:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:37: 13000000 INFO @ Sun, 21 Jun 2020 16:53:38: 8000000 INFO @ Sun, 21 Jun 2020 16:53:39: 1000000 INFO @ Sun, 21 Jun 2020 16:53:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:41: #1 total tags in treatment: 13861687 INFO @ Sun, 21 Jun 2020 16:53:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:41: #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 16:53:42: #1 tags after filtering in treatment: 13861687 INFO @ Sun, 21 Jun 2020 16:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:42: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:43: 9000000 INFO @ Sun, 21 Jun 2020 16:53:43: #2 number of paired peaks: 629 WARNING @ Sun, 21 Jun 2020 16:53:43: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Sun, 21 Jun 2020 16:53:43: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:43: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:43: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:43: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:43: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 16:53:43: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sun, 21 Jun 2020 16:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.05_model.r WARNING @ Sun, 21 Jun 2020 16:53:43: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:53:43: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sun, 21 Jun 2020 16:53:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:53:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:53:44: 2000000 INFO @ Sun, 21 Jun 2020 16:53:47: 10000000 INFO @ Sun, 21 Jun 2020 16:53:49: 3000000 INFO @ Sun, 21 Jun 2020 16:53:51: 11000000 INFO @ Sun, 21 Jun 2020 16:53:54: 4000000 INFO @ Sun, 21 Jun 2020 16:53:56: 12000000 INFO @ Sun, 21 Jun 2020 16:53:58: 5000000 INFO @ Sun, 21 Jun 2020 16:54:00: 13000000 INFO @ Sun, 21 Jun 2020 16:54:03: 6000000 INFO @ Sun, 21 Jun 2020 16:54:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:04: #1 total tags in treatment: 13861687 INFO @ Sun, 21 Jun 2020 16:54:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:04: #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 16:54:05: #1 tags after filtering in treatment: 13861687 INFO @ Sun, 21 Jun 2020 16:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:05: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:06: #2 number of paired peaks: 629 WARNING @ Sun, 21 Jun 2020 16:54:06: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Sun, 21 Jun 2020 16:54:06: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:06: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:06: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:06: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:06: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 16:54:06: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sun, 21 Jun 2020 16:54:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.10_model.r WARNING @ Sun, 21 Jun 2020 16:54:06: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:06: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sun, 21 Jun 2020 16:54:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:54:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:54:08: 7000000 INFO @ Sun, 21 Jun 2020 16:54:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:13: 8000000 INFO @ Sun, 21 Jun 2020 16:54:17: 9000000 INFO @ Sun, 21 Jun 2020 16:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.05_summits.bed INFO @ Sun, 21 Jun 2020 16:54:21: Done! pass1 - making usageList (512 chroms): 1 millis pass2 - checking and writing primary data (2466 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:54:22: 10000000 INFO @ Sun, 21 Jun 2020 16:54:27: 11000000 INFO @ Sun, 21 Jun 2020 16:54:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:32: 12000000 INFO @ Sun, 21 Jun 2020 16:54:36: 13000000 INFO @ Sun, 21 Jun 2020 16:54:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:41: #1 total tags in treatment: 13861687 INFO @ Sun, 21 Jun 2020 16:54:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:41: #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 16:54:41: #1 tags after filtering in treatment: 13861687 INFO @ Sun, 21 Jun 2020 16:54:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:41: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:42: #2 number of paired peaks: 629 WARNING @ Sun, 21 Jun 2020 16:54:42: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Sun, 21 Jun 2020 16:54:42: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:42: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:42: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:42: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:42: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 16:54:42: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sun, 21 Jun 2020 16:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.20_model.r WARNING @ Sun, 21 Jun 2020 16:54:42: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:42: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sun, 21 Jun 2020 16:54:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:54:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.10_summits.bed INFO @ Sun, 21 Jun 2020 16:54:43: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (1906 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:55:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:55:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041385/SRX041385.20_summits.bed INFO @ Sun, 21 Jun 2020 16:55:21: Done! pass1 - making usageList (264 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 8 millis CompletedMACS2peakCalling