Job ID = 6529385 SRX = SRX2325647 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: 00:17:42 47011860 reads; of these: 47011860 (100.00%) were unpaired; of these: 6295999 (13.39%) aligned 0 times 31111511 (66.18%) aligned exactly 1 time 9604350 (20.43%) aligned >1 times 86.61% overall alignment rate Time searching: 00:17:42 Overall time: 00:17:42 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 20 files... [bam_rmdupse_core] 8237952 / 40715861 = 0.2023 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 02:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.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 02:11:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:11:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:11:16: 1000000 INFO @ Tue, 30 Jun 2020 02:11:22: 2000000 INFO @ Tue, 30 Jun 2020 02:11:28: 3000000 INFO @ Tue, 30 Jun 2020 02:11:34: 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 02:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.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 02:11:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:11:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:11:41: 5000000 INFO @ Tue, 30 Jun 2020 02:11:47: 1000000 INFO @ Tue, 30 Jun 2020 02:11:48: 6000000 INFO @ Tue, 30 Jun 2020 02:11:54: 2000000 INFO @ Tue, 30 Jun 2020 02:11:55: 7000000 INFO @ Tue, 30 Jun 2020 02:12:01: 3000000 INFO @ Tue, 30 Jun 2020 02:12:02: 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 @ Tue, 30 Jun 2020 02:12:07: 4000000 INFO @ Tue, 30 Jun 2020 02:12:09: 9000000 INFO @ Tue, 30 Jun 2020 02:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.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 02:12:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:12:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:12:15: 5000000 INFO @ Tue, 30 Jun 2020 02:12:16: 10000000 INFO @ Tue, 30 Jun 2020 02:12:17: 1000000 INFO @ Tue, 30 Jun 2020 02:12:22: 6000000 INFO @ Tue, 30 Jun 2020 02:12:23: 2000000 INFO @ Tue, 30 Jun 2020 02:12:24: 11000000 INFO @ Tue, 30 Jun 2020 02:12:30: 7000000 INFO @ Tue, 30 Jun 2020 02:12:30: 3000000 INFO @ Tue, 30 Jun 2020 02:12:31: 12000000 INFO @ Tue, 30 Jun 2020 02:12:37: 4000000 INFO @ Tue, 30 Jun 2020 02:12:37: 8000000 INFO @ Tue, 30 Jun 2020 02:12:39: 13000000 INFO @ Tue, 30 Jun 2020 02:12:44: 5000000 INFO @ Tue, 30 Jun 2020 02:12:45: 9000000 INFO @ Tue, 30 Jun 2020 02:12:46: 14000000 INFO @ Tue, 30 Jun 2020 02:12:51: 6000000 INFO @ Tue, 30 Jun 2020 02:12:53: 10000000 INFO @ Tue, 30 Jun 2020 02:12:54: 15000000 INFO @ Tue, 30 Jun 2020 02:12:58: 7000000 INFO @ Tue, 30 Jun 2020 02:13:00: 11000000 INFO @ Tue, 30 Jun 2020 02:13:01: 16000000 INFO @ Tue, 30 Jun 2020 02:13:05: 8000000 INFO @ Tue, 30 Jun 2020 02:13:08: 12000000 INFO @ Tue, 30 Jun 2020 02:13:08: 17000000 INFO @ Tue, 30 Jun 2020 02:13:11: 9000000 INFO @ Tue, 30 Jun 2020 02:13:15: 13000000 INFO @ Tue, 30 Jun 2020 02:13:16: 18000000 INFO @ Tue, 30 Jun 2020 02:13:18: 10000000 INFO @ Tue, 30 Jun 2020 02:13:22: 14000000 INFO @ Tue, 30 Jun 2020 02:13:23: 19000000 INFO @ Tue, 30 Jun 2020 02:13:25: 11000000 INFO @ Tue, 30 Jun 2020 02:13:29: 15000000 INFO @ Tue, 30 Jun 2020 02:13:30: 20000000 INFO @ Tue, 30 Jun 2020 02:13:32: 12000000 INFO @ Tue, 30 Jun 2020 02:13:37: 16000000 INFO @ Tue, 30 Jun 2020 02:13:37: 21000000 INFO @ Tue, 30 Jun 2020 02:13:38: 13000000 INFO @ Tue, 30 Jun 2020 02:13:44: 17000000 INFO @ Tue, 30 Jun 2020 02:13:45: 22000000 INFO @ Tue, 30 Jun 2020 02:13:45: 14000000 INFO @ Tue, 30 Jun 2020 02:13:51: 18000000 INFO @ Tue, 30 Jun 2020 02:13:52: 15000000 INFO @ Tue, 30 Jun 2020 02:13:52: 23000000 INFO @ Tue, 30 Jun 2020 02:13:58: 19000000 INFO @ Tue, 30 Jun 2020 02:13:59: 24000000 INFO @ Tue, 30 Jun 2020 02:14:00: 16000000 INFO @ Tue, 30 Jun 2020 02:14:06: 20000000 INFO @ Tue, 30 Jun 2020 02:14:06: 17000000 INFO @ Tue, 30 Jun 2020 02:14:07: 25000000 INFO @ Tue, 30 Jun 2020 02:14:13: 21000000 INFO @ Tue, 30 Jun 2020 02:14:13: 18000000 INFO @ Tue, 30 Jun 2020 02:14:14: 26000000 INFO @ Tue, 30 Jun 2020 02:14:20: 19000000 INFO @ Tue, 30 Jun 2020 02:14:21: 22000000 INFO @ Tue, 30 Jun 2020 02:14:22: 27000000 INFO @ Tue, 30 Jun 2020 02:14:27: 20000000 INFO @ Tue, 30 Jun 2020 02:14:28: 23000000 INFO @ Tue, 30 Jun 2020 02:14:30: 28000000 INFO @ Tue, 30 Jun 2020 02:14:34: 21000000 INFO @ Tue, 30 Jun 2020 02:14:36: 24000000 INFO @ Tue, 30 Jun 2020 02:14:38: 29000000 INFO @ Tue, 30 Jun 2020 02:14:41: 22000000 INFO @ Tue, 30 Jun 2020 02:14:43: 25000000 INFO @ Tue, 30 Jun 2020 02:14:46: 30000000 INFO @ Tue, 30 Jun 2020 02:14:47: 23000000 INFO @ Tue, 30 Jun 2020 02:14:51: 26000000 INFO @ Tue, 30 Jun 2020 02:14:53: 31000000 INFO @ Tue, 30 Jun 2020 02:14:54: 24000000 INFO @ Tue, 30 Jun 2020 02:14:58: 27000000 INFO @ Tue, 30 Jun 2020 02:15:01: 32000000 INFO @ Tue, 30 Jun 2020 02:15:01: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:15:04: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:15:04: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:15:04: #1 total tags in treatment: 32477909 INFO @ Tue, 30 Jun 2020 02:15:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:04: #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 02:15:06: #1 tags after filtering in treatment: 32477906 INFO @ Tue, 30 Jun 2020 02:15:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:06: 28000000 INFO @ Tue, 30 Jun 2020 02:15:07: 26000000 INFO @ Tue, 30 Jun 2020 02:15:08: #2 number of paired peaks: 120 WARNING @ Tue, 30 Jun 2020 02:15:08: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:08: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:15:08: #2 alternative fragment length(s) may be 2,81 bps INFO @ Tue, 30 Jun 2020 02:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.05_model.r WARNING @ Tue, 30 Jun 2020 02:15:08: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:08: #2 You may need to consider one of the other alternative d(s): 2,81 WARNING @ Tue, 30 Jun 2020 02:15:08: #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 02:15:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:12: 29000000 INFO @ Tue, 30 Jun 2020 02:15:14: 27000000 INFO @ Tue, 30 Jun 2020 02:15:19: 30000000 INFO @ Tue, 30 Jun 2020 02:15:22: 28000000 INFO @ Tue, 30 Jun 2020 02:15:25: 31000000 INFO @ Tue, 30 Jun 2020 02:15:28: 29000000 INFO @ Tue, 30 Jun 2020 02:15:32: 32000000 INFO @ Tue, 30 Jun 2020 02:15:35: 30000000 INFO @ Tue, 30 Jun 2020 02:15:36: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:15:36: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:15:36: #1 total tags in treatment: 32477909 INFO @ Tue, 30 Jun 2020 02:15:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:36: #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 02:15:37: #1 tags after filtering in treatment: 32477906 INFO @ Tue, 30 Jun 2020 02:15:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:39: #2 number of paired peaks: 120 WARNING @ Tue, 30 Jun 2020 02:15:39: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:39: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:15:39: #2 alternative fragment length(s) may be 2,81 bps INFO @ Tue, 30 Jun 2020 02:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.10_model.r WARNING @ Tue, 30 Jun 2020 02:15:39: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:39: #2 You may need to consider one of the other alternative d(s): 2,81 WARNING @ Tue, 30 Jun 2020 02:15:39: #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 02:15:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:41: 31000000 INFO @ Tue, 30 Jun 2020 02:15:48: 32000000 INFO @ Tue, 30 Jun 2020 02:15:51: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:15:51: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:15:51: #1 total tags in treatment: 32477909 INFO @ Tue, 30 Jun 2020 02:15:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:51: #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 02:15:53: #1 tags after filtering in treatment: 32477906 INFO @ Tue, 30 Jun 2020 02:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:55: #2 number of paired peaks: 120 WARNING @ Tue, 30 Jun 2020 02:15:55: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:55: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:15:55: #2 alternative fragment length(s) may be 2,81 bps INFO @ Tue, 30 Jun 2020 02:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.20_model.r WARNING @ Tue, 30 Jun 2020 02:15:55: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:55: #2 You may need to consider one of the other alternative d(s): 2,81 WARNING @ Tue, 30 Jun 2020 02:15:55: #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 02:15:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.05_summits.bed INFO @ Tue, 30 Jun 2020 02:16:25: Done! pass1 - making usageList (811 chroms): 2 millis pass2 - checking and writing primary data (3009 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:16:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.10_summits.bed INFO @ Tue, 30 Jun 2020 02:16:56: Done! pass1 - making usageList (659 chroms): 1 millis pass2 - checking and writing primary data (1769 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325647/SRX2325647.20_summits.bed INFO @ Tue, 30 Jun 2020 02:17:09: Done! pass1 - making usageList (382 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 21 millis CompletedMACS2peakCalling