Job ID = 6455353 SRX = SRX287718 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:01:41 prefetch.2.10.7: 1) Downloading 'SRR869907'... 2020-06-21T10:01:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:03:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:03:24 prefetch.2.10.7: 1) 'SRR869907' was downloaded successfully Read 17853523 spots for SRR869907/SRR869907.sra Written 17853523 spots for SRR869907/SRR869907.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: 00:00:01 Multiseed full-index search: 00:04:46 17853523 reads; of these: 17853523 (100.00%) were unpaired; of these: 1216162 (6.81%) aligned 0 times 13315447 (74.58%) aligned exactly 1 time 3321914 (18.61%) aligned >1 times 93.19% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 1617765 / 16637361 = 0.0972 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 19:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.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 19:13:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:40: 1000000 INFO @ Sun, 21 Jun 2020 19:13:46: 2000000 INFO @ Sun, 21 Jun 2020 19:13:52: 3000000 INFO @ Sun, 21 Jun 2020 19:13:57: 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 19:14:03: 5000000 INFO @ Sun, 21 Jun 2020 19:14:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.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 19:14:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:09: 6000000 INFO @ Sun, 21 Jun 2020 19:14:10: 1000000 INFO @ Sun, 21 Jun 2020 19:14:15: 7000000 INFO @ Sun, 21 Jun 2020 19:14:17: 2000000 INFO @ Sun, 21 Jun 2020 19:14:21: 8000000 INFO @ Sun, 21 Jun 2020 19:14:24: 3000000 INFO @ Sun, 21 Jun 2020 19:14:28: 9000000 INFO @ Sun, 21 Jun 2020 19:14:30: 4000000 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 19:14:34: 10000000 INFO @ Sun, 21 Jun 2020 19:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.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 19:14:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:37: 5000000 INFO @ Sun, 21 Jun 2020 19:14:40: 11000000 INFO @ Sun, 21 Jun 2020 19:14:40: 1000000 INFO @ Sun, 21 Jun 2020 19:14:43: 6000000 INFO @ Sun, 21 Jun 2020 19:14:46: 12000000 INFO @ Sun, 21 Jun 2020 19:14:46: 2000000 INFO @ Sun, 21 Jun 2020 19:14:50: 7000000 INFO @ Sun, 21 Jun 2020 19:14:52: 3000000 INFO @ Sun, 21 Jun 2020 19:14:53: 13000000 INFO @ Sun, 21 Jun 2020 19:14:57: 8000000 INFO @ Sun, 21 Jun 2020 19:14:59: 4000000 INFO @ Sun, 21 Jun 2020 19:14:59: 14000000 INFO @ Sun, 21 Jun 2020 19:15:03: 9000000 INFO @ Sun, 21 Jun 2020 19:15:05: 5000000 INFO @ Sun, 21 Jun 2020 19:15:05: 15000000 INFO @ Sun, 21 Jun 2020 19:15:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:06: #1 total tags in treatment: 15019596 INFO @ Sun, 21 Jun 2020 19:15:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:06: #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 19:15:06: #1 tags after filtering in treatment: 15019594 INFO @ Sun, 21 Jun 2020 19:15:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:07: #2 number of paired peaks: 216 WARNING @ Sun, 21 Jun 2020 19:15:07: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:07: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:15:07: #2 alternative fragment length(s) may be 4,43,521 bps INFO @ Sun, 21 Jun 2020 19:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.05_model.r WARNING @ Sun, 21 Jun 2020 19:15:07: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:07: #2 You may need to consider one of the other alternative d(s): 4,43,521 WARNING @ Sun, 21 Jun 2020 19:15:07: #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 19:15:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:10: 10000000 INFO @ Sun, 21 Jun 2020 19:15:11: 6000000 INFO @ Sun, 21 Jun 2020 19:15:17: 7000000 INFO @ Sun, 21 Jun 2020 19:15:17: 11000000 INFO @ Sun, 21 Jun 2020 19:15:23: 8000000 INFO @ Sun, 21 Jun 2020 19:15:23: 12000000 INFO @ Sun, 21 Jun 2020 19:15:29: 9000000 INFO @ Sun, 21 Jun 2020 19:15:30: 13000000 INFO @ Sun, 21 Jun 2020 19:15:35: 10000000 INFO @ Sun, 21 Jun 2020 19:15:37: 14000000 INFO @ Sun, 21 Jun 2020 19:15:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:41: 11000000 INFO @ Sun, 21 Jun 2020 19:15:44: 15000000 INFO @ Sun, 21 Jun 2020 19:15:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:44: #1 total tags in treatment: 15019596 INFO @ Sun, 21 Jun 2020 19:15:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:44: #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 19:15:45: #1 tags after filtering in treatment: 15019594 INFO @ Sun, 21 Jun 2020 19:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:46: #2 number of paired peaks: 216 WARNING @ Sun, 21 Jun 2020 19:15:46: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:46: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:15:46: #2 alternative fragment length(s) may be 4,43,521 bps INFO @ Sun, 21 Jun 2020 19:15:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.10_model.r WARNING @ Sun, 21 Jun 2020 19:15:46: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:46: #2 You may need to consider one of the other alternative d(s): 4,43,521 WARNING @ Sun, 21 Jun 2020 19:15:46: #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 19:15:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:48: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:54: Done! INFO @ Sun, 21 Jun 2020 19:15:54: 13000000 pass1 - making usageList (477 chroms): 1 millis pass2 - checking and writing primary data (1940 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:00: 14000000 INFO @ Sun, 21 Jun 2020 19:16:06: 15000000 INFO @ Sun, 21 Jun 2020 19:16:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:06: #1 total tags in treatment: 15019596 INFO @ Sun, 21 Jun 2020 19:16:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:06: #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 19:16:06: #1 tags after filtering in treatment: 15019594 INFO @ Sun, 21 Jun 2020 19:16:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:07: #2 number of paired peaks: 216 WARNING @ Sun, 21 Jun 2020 19:16:07: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:08: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:16:08: #2 alternative fragment length(s) may be 4,43,521 bps INFO @ Sun, 21 Jun 2020 19:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.20_model.r WARNING @ Sun, 21 Jun 2020 19:16:08: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:08: #2 You may need to consider one of the other alternative d(s): 4,43,521 WARNING @ Sun, 21 Jun 2020 19:16:08: #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 19:16:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:30: Done! pass1 - making usageList (337 chroms): 1 millis pass2 - checking and writing primary data (845 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287718/SRX287718.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:54: Done! pass1 - making usageList (166 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 8 millis CompletedMACS2peakCalling