Job ID = 6529676 SRX = SRX3981650 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: 00:11:23 36477931 reads; of these: 36477931 (100.00%) were unpaired; of these: 1041036 (2.85%) aligned 0 times 26040558 (71.39%) aligned exactly 1 time 9396337 (25.76%) aligned >1 times 97.15% overall alignment rate Time searching: 00:11:23 Overall time: 00:11:23 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] 5164973 / 35436895 = 0.1458 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 02:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.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 02:57:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:36: 1000000 INFO @ Tue, 30 Jun 2020 02:57:43: 2000000 INFO @ Tue, 30 Jun 2020 02:57:49: 3000000 INFO @ Tue, 30 Jun 2020 02:57:55: 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 @ Tue, 30 Jun 2020 02:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.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 02:58:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:01: 5000000 INFO @ Tue, 30 Jun 2020 02:58:08: 1000000 INFO @ Tue, 30 Jun 2020 02:58:08: 6000000 INFO @ Tue, 30 Jun 2020 02:58:14: 7000000 INFO @ Tue, 30 Jun 2020 02:58:14: 2000000 INFO @ Tue, 30 Jun 2020 02:58:21: 8000000 INFO @ Tue, 30 Jun 2020 02:58:21: 3000000 INFO @ Tue, 30 Jun 2020 02:58:28: 9000000 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 02:58:28: 4000000 INFO @ Tue, 30 Jun 2020 02:58:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.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 02:58:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:35: 10000000 INFO @ Tue, 30 Jun 2020 02:58:35: 5000000 INFO @ Tue, 30 Jun 2020 02:58:37: 1000000 INFO @ Tue, 30 Jun 2020 02:58:41: 11000000 INFO @ Tue, 30 Jun 2020 02:58:43: 6000000 INFO @ Tue, 30 Jun 2020 02:58:43: 2000000 INFO @ Tue, 30 Jun 2020 02:58:48: 12000000 INFO @ Tue, 30 Jun 2020 02:58:49: 3000000 INFO @ Tue, 30 Jun 2020 02:58:50: 7000000 INFO @ Tue, 30 Jun 2020 02:58:55: 13000000 INFO @ Tue, 30 Jun 2020 02:58:56: 4000000 INFO @ Tue, 30 Jun 2020 02:58:57: 8000000 INFO @ Tue, 30 Jun 2020 02:59:02: 5000000 INFO @ Tue, 30 Jun 2020 02:59:02: 14000000 INFO @ Tue, 30 Jun 2020 02:59:05: 9000000 INFO @ Tue, 30 Jun 2020 02:59:08: 6000000 INFO @ Tue, 30 Jun 2020 02:59:09: 15000000 INFO @ Tue, 30 Jun 2020 02:59:12: 10000000 INFO @ Tue, 30 Jun 2020 02:59:15: 7000000 INFO @ Tue, 30 Jun 2020 02:59:16: 16000000 INFO @ Tue, 30 Jun 2020 02:59:19: 11000000 INFO @ Tue, 30 Jun 2020 02:59:22: 8000000 INFO @ Tue, 30 Jun 2020 02:59:23: 17000000 INFO @ Tue, 30 Jun 2020 02:59:26: 12000000 INFO @ Tue, 30 Jun 2020 02:59:28: 9000000 INFO @ Tue, 30 Jun 2020 02:59:30: 18000000 INFO @ Tue, 30 Jun 2020 02:59:34: 13000000 INFO @ Tue, 30 Jun 2020 02:59:35: 10000000 INFO @ Tue, 30 Jun 2020 02:59:37: 19000000 INFO @ Tue, 30 Jun 2020 02:59:41: 14000000 INFO @ Tue, 30 Jun 2020 02:59:42: 11000000 INFO @ Tue, 30 Jun 2020 02:59:45: 20000000 INFO @ Tue, 30 Jun 2020 02:59:48: 12000000 INFO @ Tue, 30 Jun 2020 02:59:49: 15000000 INFO @ Tue, 30 Jun 2020 02:59:52: 21000000 INFO @ Tue, 30 Jun 2020 02:59:55: 13000000 INFO @ Tue, 30 Jun 2020 02:59:56: 16000000 INFO @ Tue, 30 Jun 2020 02:59:59: 22000000 INFO @ Tue, 30 Jun 2020 03:00:02: 14000000 INFO @ Tue, 30 Jun 2020 03:00:03: 17000000 INFO @ Tue, 30 Jun 2020 03:00:06: 23000000 INFO @ Tue, 30 Jun 2020 03:00:09: 15000000 INFO @ Tue, 30 Jun 2020 03:00:11: 18000000 INFO @ Tue, 30 Jun 2020 03:00:13: 24000000 INFO @ Tue, 30 Jun 2020 03:00:16: 16000000 INFO @ Tue, 30 Jun 2020 03:00:18: 19000000 INFO @ Tue, 30 Jun 2020 03:00:20: 25000000 INFO @ Tue, 30 Jun 2020 03:00:22: 17000000 INFO @ Tue, 30 Jun 2020 03:00:26: 20000000 INFO @ Tue, 30 Jun 2020 03:00:28: 26000000 INFO @ Tue, 30 Jun 2020 03:00:29: 18000000 INFO @ Tue, 30 Jun 2020 03:00:33: 21000000 INFO @ Tue, 30 Jun 2020 03:00:35: 27000000 INFO @ Tue, 30 Jun 2020 03:00:36: 19000000 INFO @ Tue, 30 Jun 2020 03:00:41: 22000000 INFO @ Tue, 30 Jun 2020 03:00:42: 28000000 INFO @ Tue, 30 Jun 2020 03:00:43: 20000000 INFO @ Tue, 30 Jun 2020 03:00:48: 23000000 INFO @ Tue, 30 Jun 2020 03:00:49: 29000000 INFO @ Tue, 30 Jun 2020 03:00:50: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:00:55: 24000000 INFO @ Tue, 30 Jun 2020 03:00:57: 22000000 INFO @ Tue, 30 Jun 2020 03:00:57: 30000000 INFO @ Tue, 30 Jun 2020 03:00:59: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:00:59: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:00:59: #1 total tags in treatment: 30271922 INFO @ Tue, 30 Jun 2020 03:00:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:59: #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 03:01:00: #1 tags after filtering in treatment: 30271862 INFO @ Tue, 30 Jun 2020 03:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:01:00: #1 finished! INFO @ Tue, 30 Jun 2020 03:01:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:01:02: #2 number of paired peaks: 244 WARNING @ Tue, 30 Jun 2020 03:01:02: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 30 Jun 2020 03:01:02: start model_add_line... INFO @ Tue, 30 Jun 2020 03:01:02: start X-correlation... INFO @ Tue, 30 Jun 2020 03:01:02: end of X-cor INFO @ Tue, 30 Jun 2020 03:01:02: #2 finished! INFO @ Tue, 30 Jun 2020 03:01:02: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 03:01:02: #2 alternative fragment length(s) may be 1,38 bps INFO @ Tue, 30 Jun 2020 03:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.05_model.r WARNING @ Tue, 30 Jun 2020 03:01:02: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:01:02: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Tue, 30 Jun 2020 03:01:02: #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 03:01:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:01:03: 25000000 INFO @ Tue, 30 Jun 2020 03:01:03: 23000000 INFO @ Tue, 30 Jun 2020 03:01:10: 24000000 INFO @ Tue, 30 Jun 2020 03:01:10: 26000000 INFO @ Tue, 30 Jun 2020 03:01:16: 25000000 INFO @ Tue, 30 Jun 2020 03:01:17: 27000000 INFO @ Tue, 30 Jun 2020 03:01:24: 28000000 INFO @ Tue, 30 Jun 2020 03:01:24: 26000000 INFO @ Tue, 30 Jun 2020 03:01:30: 27000000 INFO @ Tue, 30 Jun 2020 03:01:31: 29000000 INFO @ Tue, 30 Jun 2020 03:01:37: 28000000 INFO @ Tue, 30 Jun 2020 03:01:38: 30000000 INFO @ Tue, 30 Jun 2020 03:01:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:01:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:01:40: #1 total tags in treatment: 30271922 INFO @ Tue, 30 Jun 2020 03:01:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:01:40: #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 03:01:41: #1 tags after filtering in treatment: 30271862 INFO @ Tue, 30 Jun 2020 03:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:01:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:01:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:01:43: #2 number of paired peaks: 244 WARNING @ Tue, 30 Jun 2020 03:01:43: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 30 Jun 2020 03:01:43: start model_add_line... INFO @ Tue, 30 Jun 2020 03:01:43: start X-correlation... INFO @ Tue, 30 Jun 2020 03:01:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:01:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:01:43: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 03:01:43: #2 alternative fragment length(s) may be 1,38 bps INFO @ Tue, 30 Jun 2020 03:01:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.10_model.r WARNING @ Tue, 30 Jun 2020 03:01:43: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:01:43: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Tue, 30 Jun 2020 03:01:43: #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 03:01:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:01:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:01:44: 29000000 INFO @ Tue, 30 Jun 2020 03:01:50: 30000000 INFO @ Tue, 30 Jun 2020 03:01:52: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:01:52: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:01:52: #1 total tags in treatment: 30271922 INFO @ Tue, 30 Jun 2020 03:01:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:01:52: #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 03:01:53: #1 tags after filtering in treatment: 30271862 INFO @ Tue, 30 Jun 2020 03:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:01:53: #1 finished! INFO @ Tue, 30 Jun 2020 03:01:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:01:55: #2 number of paired peaks: 244 WARNING @ Tue, 30 Jun 2020 03:01:55: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 30 Jun 2020 03:01:55: start model_add_line... INFO @ Tue, 30 Jun 2020 03:01:55: start X-correlation... INFO @ Tue, 30 Jun 2020 03:01:55: end of X-cor INFO @ Tue, 30 Jun 2020 03:01:55: #2 finished! INFO @ Tue, 30 Jun 2020 03:01:55: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 03:01:55: #2 alternative fragment length(s) may be 1,38 bps INFO @ Tue, 30 Jun 2020 03:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.20_model.r WARNING @ Tue, 30 Jun 2020 03:01:55: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:01:55: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Tue, 30 Jun 2020 03:01:55: #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 03:01:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:01:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.05_summits.bed INFO @ Tue, 30 Jun 2020 03:02:26: Done! pass1 - making usageList (625 chroms): 3 millis pass2 - checking and writing primary data (3072 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:02:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:02:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.10_summits.bed INFO @ Tue, 30 Jun 2020 03:03:08: Done! pass1 - making usageList (450 chroms): 1 millis pass2 - checking and writing primary data (1588 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981650/SRX3981650.20_summits.bed INFO @ Tue, 30 Jun 2020 03:03:24: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 8 millis CompletedMACS2peakCalling