Job ID = 6529679 SRX = SRX3981654 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:10:52 38865798 reads; of these: 38865798 (100.00%) were unpaired; of these: 1390368 (3.58%) aligned 0 times 27621486 (71.07%) aligned exactly 1 time 9853944 (25.35%) aligned >1 times 96.42% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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] 4891858 / 37475430 = 0.1305 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 @ Tue, 30 Jun 2020 02:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.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 @ Tue, 30 Jun 2020 02:49:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:21: 1000000 INFO @ Tue, 30 Jun 2020 02:49:28: 2000000 INFO @ Tue, 30 Jun 2020 02:49:35: 3000000 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 @ Tue, 30 Jun 2020 02:49:42: 4000000 INFO @ Tue, 30 Jun 2020 02:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.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 @ Tue, 30 Jun 2020 02:49:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:50: 5000000 INFO @ Tue, 30 Jun 2020 02:49:51: 1000000 INFO @ Tue, 30 Jun 2020 02:49:58: 2000000 INFO @ Tue, 30 Jun 2020 02:49:59: 6000000 INFO @ Tue, 30 Jun 2020 02:50:06: 3000000 INFO @ Tue, 30 Jun 2020 02:50:07: 7000000 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 @ Tue, 30 Jun 2020 02:50:13: 4000000 INFO @ Tue, 30 Jun 2020 02:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.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 @ Tue, 30 Jun 2020 02:50:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:15: 8000000 INFO @ Tue, 30 Jun 2020 02:50:21: 5000000 INFO @ Tue, 30 Jun 2020 02:50:22: 1000000 INFO @ Tue, 30 Jun 2020 02:50:23: 9000000 INFO @ Tue, 30 Jun 2020 02:50:28: 6000000 INFO @ Tue, 30 Jun 2020 02:50:30: 2000000 INFO @ Tue, 30 Jun 2020 02:50:32: 10000000 INFO @ Tue, 30 Jun 2020 02:50:35: 7000000 INFO @ Tue, 30 Jun 2020 02:50:39: 3000000 INFO @ Tue, 30 Jun 2020 02:50:40: 11000000 INFO @ Tue, 30 Jun 2020 02:50:43: 8000000 INFO @ Tue, 30 Jun 2020 02:50:47: 4000000 INFO @ Tue, 30 Jun 2020 02:50:48: 12000000 INFO @ Tue, 30 Jun 2020 02:50:50: 9000000 INFO @ Tue, 30 Jun 2020 02:50:55: 5000000 INFO @ Tue, 30 Jun 2020 02:50:57: 13000000 INFO @ Tue, 30 Jun 2020 02:50:58: 10000000 INFO @ Tue, 30 Jun 2020 02:51:04: 6000000 INFO @ Tue, 30 Jun 2020 02:51:05: 14000000 INFO @ Tue, 30 Jun 2020 02:51:05: 11000000 INFO @ Tue, 30 Jun 2020 02:51:12: 7000000 INFO @ Tue, 30 Jun 2020 02:51:13: 12000000 INFO @ Tue, 30 Jun 2020 02:51:13: 15000000 INFO @ Tue, 30 Jun 2020 02:51:20: 13000000 INFO @ Tue, 30 Jun 2020 02:51:21: 8000000 INFO @ Tue, 30 Jun 2020 02:51:22: 16000000 INFO @ Tue, 30 Jun 2020 02:51:28: 14000000 INFO @ Tue, 30 Jun 2020 02:51:29: 9000000 INFO @ Tue, 30 Jun 2020 02:51:30: 17000000 INFO @ Tue, 30 Jun 2020 02:51:35: 15000000 INFO @ Tue, 30 Jun 2020 02:51:37: 10000000 INFO @ Tue, 30 Jun 2020 02:51:39: 18000000 INFO @ Tue, 30 Jun 2020 02:51:43: 16000000 INFO @ Tue, 30 Jun 2020 02:51:46: 11000000 INFO @ Tue, 30 Jun 2020 02:51:47: 19000000 INFO @ Tue, 30 Jun 2020 02:51:50: 17000000 INFO @ Tue, 30 Jun 2020 02:51:54: 12000000 INFO @ Tue, 30 Jun 2020 02:51:55: 20000000 INFO @ Tue, 30 Jun 2020 02:51:58: 18000000 INFO @ Tue, 30 Jun 2020 02:52:02: 13000000 INFO @ Tue, 30 Jun 2020 02:52:04: 21000000 INFO @ Tue, 30 Jun 2020 02:52:06: 19000000 INFO @ Tue, 30 Jun 2020 02:52:11: 14000000 INFO @ Tue, 30 Jun 2020 02:52:12: 22000000 INFO @ Tue, 30 Jun 2020 02:52:13: 20000000 INFO @ Tue, 30 Jun 2020 02:52:19: 15000000 INFO @ Tue, 30 Jun 2020 02:52:20: 23000000 INFO @ Tue, 30 Jun 2020 02:52:20: 21000000 INFO @ Tue, 30 Jun 2020 02:52:27: 16000000 INFO @ Tue, 30 Jun 2020 02:52:28: 22000000 INFO @ Tue, 30 Jun 2020 02:52:28: 24000000 INFO @ Tue, 30 Jun 2020 02:52:35: 23000000 INFO @ Tue, 30 Jun 2020 02:52:35: 17000000 INFO @ Tue, 30 Jun 2020 02:52:37: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:52:43: 24000000 INFO @ Tue, 30 Jun 2020 02:52:44: 18000000 INFO @ Tue, 30 Jun 2020 02:52:45: 26000000 INFO @ Tue, 30 Jun 2020 02:52:50: 25000000 INFO @ Tue, 30 Jun 2020 02:52:52: 19000000 INFO @ Tue, 30 Jun 2020 02:52:53: 27000000 INFO @ Tue, 30 Jun 2020 02:52:58: 26000000 INFO @ Tue, 30 Jun 2020 02:53:00: 20000000 INFO @ Tue, 30 Jun 2020 02:53:02: 28000000 INFO @ Tue, 30 Jun 2020 02:53:05: 27000000 INFO @ Tue, 30 Jun 2020 02:53:08: 21000000 INFO @ Tue, 30 Jun 2020 02:53:10: 29000000 INFO @ Tue, 30 Jun 2020 02:53:13: 28000000 INFO @ Tue, 30 Jun 2020 02:53:17: 22000000 INFO @ Tue, 30 Jun 2020 02:53:18: 30000000 INFO @ Tue, 30 Jun 2020 02:53:20: 29000000 INFO @ Tue, 30 Jun 2020 02:53:25: 23000000 INFO @ Tue, 30 Jun 2020 02:53:27: 31000000 INFO @ Tue, 30 Jun 2020 02:53:28: 30000000 INFO @ Tue, 30 Jun 2020 02:53:33: 24000000 INFO @ Tue, 30 Jun 2020 02:53:35: 32000000 INFO @ Tue, 30 Jun 2020 02:53:35: 31000000 INFO @ Tue, 30 Jun 2020 02:53:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:53:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:53:40: #1 total tags in treatment: 32583572 INFO @ Tue, 30 Jun 2020 02:53:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:53:41: #1 tags after filtering in treatment: 32583522 INFO @ Tue, 30 Jun 2020 02:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:41: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:42: 25000000 INFO @ Tue, 30 Jun 2020 02:53:43: #2 number of paired peaks: 184 WARNING @ Tue, 30 Jun 2020 02:53:43: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:43: 32000000 INFO @ Tue, 30 Jun 2020 02:53:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:43: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:53:43: #2 alternative fragment length(s) may be 1,46,534,580 bps INFO @ Tue, 30 Jun 2020 02:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.05_model.r WARNING @ Tue, 30 Jun 2020 02:53:43: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:43: #2 You may need to consider one of the other alternative d(s): 1,46,534,580 WARNING @ Tue, 30 Jun 2020 02:53:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:53:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:48: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:53:48: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:53:48: #1 total tags in treatment: 32583572 INFO @ Tue, 30 Jun 2020 02:53:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:53:48: #1 tags after filtering in treatment: 32583522 INFO @ Tue, 30 Jun 2020 02:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:50: 26000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:53:50: #2 number of paired peaks: 184 WARNING @ Tue, 30 Jun 2020 02:53:50: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:51: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:53:51: #2 alternative fragment length(s) may be 1,46,534,580 bps INFO @ Tue, 30 Jun 2020 02:53:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.10_model.r WARNING @ Tue, 30 Jun 2020 02:53:51: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:51: #2 You may need to consider one of the other alternative d(s): 1,46,534,580 WARNING @ Tue, 30 Jun 2020 02:53:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:53:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:57: 27000000 INFO @ Tue, 30 Jun 2020 02:54:04: 28000000 INFO @ Tue, 30 Jun 2020 02:54:12: 29000000 INFO @ Tue, 30 Jun 2020 02:54:19: 30000000 INFO @ Tue, 30 Jun 2020 02:54:26: 31000000 INFO @ Tue, 30 Jun 2020 02:54:33: 32000000 INFO @ Tue, 30 Jun 2020 02:54:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:37: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:54:37: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:54:37: #1 total tags in treatment: 32583572 INFO @ Tue, 30 Jun 2020 02:54:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:54:38: #1 tags after filtering in treatment: 32583522 INFO @ Tue, 30 Jun 2020 02:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:38: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:40: #2 number of paired peaks: 184 WARNING @ Tue, 30 Jun 2020 02:54:40: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:40: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:54:40: #2 alternative fragment length(s) may be 1,46,534,580 bps INFO @ Tue, 30 Jun 2020 02:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.20_model.r WARNING @ Tue, 30 Jun 2020 02:54:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:40: #2 You may need to consider one of the other alternative d(s): 1,46,534,580 WARNING @ Tue, 30 Jun 2020 02:54:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:54:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.05_summits.bed INFO @ Tue, 30 Jun 2020 02:55:01: Done! pass1 - making usageList (631 chroms): 1 millis pass2 - checking and writing primary data (3069 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.10_summits.bed INFO @ Tue, 30 Jun 2020 02:55:06: Done! pass1 - making usageList (491 chroms): 2 millis pass2 - checking and writing primary data (1927 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981654/SRX3981654.20_summits.bed INFO @ Tue, 30 Jun 2020 02:55:57: Done! pass1 - making usageList (258 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 9 millis CompletedMACS2peakCalling