Job ID = 6454487 SRX = SRX2165274 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:09 prefetch.2.10.7: 1) Downloading 'SRR4244777'... 2020-06-21T09:15:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:33 prefetch.2.10.7: 1) 'SRR4244777' was downloaded successfully Read 25760057 spots for SRR4244777/SRR4244777.sra Written 25760057 spots for SRR4244777/SRR4244777.sra 2020-06-21T09:21:59 prefetch.2.10.7: 1) Downloading 'SRR4244778'... 2020-06-21T09:21:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:29:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:29:45 prefetch.2.10.7: 1) 'SRR4244778' was downloaded successfully Read 22088064 spots for SRR4244778/SRR4244778.sra Written 22088064 spots for SRR4244778/SRR4244778.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: 00:12:39 47848121 reads; of these: 47848121 (100.00%) were unpaired; of these: 18078161 (37.78%) aligned 0 times 21475001 (44.88%) aligned exactly 1 time 8294959 (17.34%) aligned >1 times 62.22% overall alignment rate Time searching: 00:12:39 Overall time: 00:12:39 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 16 files... [bam_rmdupse_core] 16377540 / 29769960 = 0.5501 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 18:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.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 18:51:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:06: 1000000 INFO @ Sun, 21 Jun 2020 18:52:13: 2000000 INFO @ Sun, 21 Jun 2020 18:52:19: 3000000 INFO @ Sun, 21 Jun 2020 18:52:26: 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 18:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.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 18:52:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:33: 5000000 INFO @ Sun, 21 Jun 2020 18:52:37: 1000000 INFO @ Sun, 21 Jun 2020 18:52:40: 6000000 INFO @ Sun, 21 Jun 2020 18:52:44: 2000000 INFO @ Sun, 21 Jun 2020 18:52:48: 7000000 INFO @ Sun, 21 Jun 2020 18:52:51: 3000000 INFO @ Sun, 21 Jun 2020 18:52:55: 8000000 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 18:52:59: 4000000 INFO @ Sun, 21 Jun 2020 18:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.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 18:52:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:02: 9000000 INFO @ Sun, 21 Jun 2020 18:53:06: 5000000 INFO @ Sun, 21 Jun 2020 18:53:07: 1000000 INFO @ Sun, 21 Jun 2020 18:53:10: 10000000 INFO @ Sun, 21 Jun 2020 18:53:13: 6000000 INFO @ Sun, 21 Jun 2020 18:53:14: 2000000 INFO @ Sun, 21 Jun 2020 18:53:17: 11000000 INFO @ Sun, 21 Jun 2020 18:53:21: 7000000 INFO @ Sun, 21 Jun 2020 18:53:21: 3000000 INFO @ Sun, 21 Jun 2020 18:53:25: 12000000 INFO @ Sun, 21 Jun 2020 18:53:28: 8000000 INFO @ Sun, 21 Jun 2020 18:53:28: 4000000 INFO @ Sun, 21 Jun 2020 18:53:32: 13000000 INFO @ Sun, 21 Jun 2020 18:53:35: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:53:35: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:53:35: #1 total tags in treatment: 13392420 INFO @ Sun, 21 Jun 2020 18:53:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:35: #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 18:53:35: 9000000 INFO @ Sun, 21 Jun 2020 18:53:35: #1 tags after filtering in treatment: 13392418 INFO @ Sun, 21 Jun 2020 18:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:36: 5000000 INFO @ Sun, 21 Jun 2020 18:53:36: #2 number of paired peaks: 1076 INFO @ Sun, 21 Jun 2020 18:53:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:36: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:53:36: #2 alternative fragment length(s) may be 3,60,598 bps INFO @ Sun, 21 Jun 2020 18:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.05_model.r WARNING @ Sun, 21 Jun 2020 18:53:36: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:36: #2 You may need to consider one of the other alternative d(s): 3,60,598 WARNING @ Sun, 21 Jun 2020 18:53:36: #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 18:53:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:42: 10000000 INFO @ Sun, 21 Jun 2020 18:53:43: 6000000 INFO @ Sun, 21 Jun 2020 18:53:49: 11000000 INFO @ Sun, 21 Jun 2020 18:53:50: 7000000 INFO @ Sun, 21 Jun 2020 18:53:56: 12000000 INFO @ Sun, 21 Jun 2020 18:53:58: 8000000 INFO @ Sun, 21 Jun 2020 18:54:03: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:54:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:05: 9000000 INFO @ Sun, 21 Jun 2020 18:54:06: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:54:06: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:54:06: #1 total tags in treatment: 13392420 INFO @ Sun, 21 Jun 2020 18:54:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:06: #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 18:54:07: #1 tags after filtering in treatment: 13392418 INFO @ Sun, 21 Jun 2020 18:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:08: #2 number of paired peaks: 1076 INFO @ Sun, 21 Jun 2020 18:54:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:08: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:54:08: #2 alternative fragment length(s) may be 3,60,598 bps INFO @ Sun, 21 Jun 2020 18:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.10_model.r WARNING @ Sun, 21 Jun 2020 18:54:08: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:08: #2 You may need to consider one of the other alternative d(s): 3,60,598 WARNING @ Sun, 21 Jun 2020 18:54:08: #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 18:54:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:12: 10000000 INFO @ Sun, 21 Jun 2020 18:54:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.05_summits.bed INFO @ Sun, 21 Jun 2020 18:54:18: Done! pass1 - making usageList (767 chroms): 2 millis pass2 - checking and writing primary data (3028 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:19: 11000000 INFO @ Sun, 21 Jun 2020 18:54:26: 12000000 INFO @ Sun, 21 Jun 2020 18:54:33: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:54:36: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:54:36: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:54:36: #1 total tags in treatment: 13392420 INFO @ Sun, 21 Jun 2020 18:54:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:36: #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 18:54:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:36: #1 tags after filtering in treatment: 13392418 INFO @ Sun, 21 Jun 2020 18:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:37: #2 number of paired peaks: 1076 INFO @ Sun, 21 Jun 2020 18:54:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:37: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:54:37: #2 alternative fragment length(s) may be 3,60,598 bps INFO @ Sun, 21 Jun 2020 18:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.20_model.r WARNING @ Sun, 21 Jun 2020 18:54:37: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:37: #2 You may need to consider one of the other alternative d(s): 3,60,598 WARNING @ Sun, 21 Jun 2020 18:54:37: #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 18:54:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:50: Done! pass1 - making usageList (646 chroms): 1 millis pass2 - checking and writing primary data (2186 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165274/SRX2165274.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:19: Done! pass1 - making usageList (500 chroms): 1 millis pass2 - checking and writing primary data (1434 records, 4 fields): 15 millis CompletedMACS2peakCalling