Job ID = 6529411 SRX = SRX2564144 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: 00:15:29 38847845 reads; of these: 38847845 (100.00%) were unpaired; of these: 2029092 (5.22%) aligned 0 times 28934975 (74.48%) aligned exactly 1 time 7883778 (20.29%) aligned >1 times 94.78% overall alignment rate Time searching: 00:15:29 Overall time: 00:15:29 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] 5695544 / 36818753 = 0.1547 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 02:09:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.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 02:09:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:53: 1000000 INFO @ Tue, 30 Jun 2020 02:10:01: 2000000 INFO @ Tue, 30 Jun 2020 02:10:09: 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 02:10:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.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 02:10:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:10:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:10:16: 4000000 INFO @ Tue, 30 Jun 2020 02:10:24: 1000000 INFO @ Tue, 30 Jun 2020 02:10:24: 5000000 INFO @ Tue, 30 Jun 2020 02:10:32: 6000000 INFO @ Tue, 30 Jun 2020 02:10:33: 2000000 INFO @ Tue, 30 Jun 2020 02:10:40: 7000000 INFO @ Tue, 30 Jun 2020 02:10:42: 3000000 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 02:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.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 02:10:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:10:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:10:48: 8000000 INFO @ Tue, 30 Jun 2020 02:10:50: 4000000 INFO @ Tue, 30 Jun 2020 02:10:54: 1000000 INFO @ Tue, 30 Jun 2020 02:10:56: 9000000 INFO @ Tue, 30 Jun 2020 02:10:58: 5000000 INFO @ Tue, 30 Jun 2020 02:11:03: 2000000 INFO @ Tue, 30 Jun 2020 02:11:04: 10000000 INFO @ Tue, 30 Jun 2020 02:11:07: 6000000 INFO @ Tue, 30 Jun 2020 02:11:12: 3000000 INFO @ Tue, 30 Jun 2020 02:11:12: 11000000 INFO @ Tue, 30 Jun 2020 02:11:15: 7000000 INFO @ Tue, 30 Jun 2020 02:11:20: 4000000 INFO @ Tue, 30 Jun 2020 02:11:20: 12000000 INFO @ Tue, 30 Jun 2020 02:11:23: 8000000 INFO @ Tue, 30 Jun 2020 02:11:29: 13000000 INFO @ Tue, 30 Jun 2020 02:11:30: 5000000 INFO @ Tue, 30 Jun 2020 02:11:31: 9000000 INFO @ Tue, 30 Jun 2020 02:11:37: 14000000 INFO @ Tue, 30 Jun 2020 02:11:38: 6000000 INFO @ Tue, 30 Jun 2020 02:11:40: 10000000 INFO @ Tue, 30 Jun 2020 02:11:45: 15000000 INFO @ Tue, 30 Jun 2020 02:11:47: 7000000 INFO @ Tue, 30 Jun 2020 02:11:48: 11000000 INFO @ Tue, 30 Jun 2020 02:11:53: 16000000 INFO @ Tue, 30 Jun 2020 02:11:55: 8000000 INFO @ Tue, 30 Jun 2020 02:11:56: 12000000 INFO @ Tue, 30 Jun 2020 02:12:01: 17000000 INFO @ Tue, 30 Jun 2020 02:12:03: 9000000 INFO @ Tue, 30 Jun 2020 02:12:04: 13000000 INFO @ Tue, 30 Jun 2020 02:12:10: 18000000 INFO @ Tue, 30 Jun 2020 02:12:11: 10000000 INFO @ Tue, 30 Jun 2020 02:12:12: 14000000 INFO @ Tue, 30 Jun 2020 02:12:18: 19000000 INFO @ Tue, 30 Jun 2020 02:12:18: 11000000 INFO @ Tue, 30 Jun 2020 02:12:20: 15000000 INFO @ Tue, 30 Jun 2020 02:12:26: 12000000 INFO @ Tue, 30 Jun 2020 02:12:26: 20000000 INFO @ Tue, 30 Jun 2020 02:12:29: 16000000 INFO @ Tue, 30 Jun 2020 02:12:33: 13000000 INFO @ Tue, 30 Jun 2020 02:12:34: 21000000 INFO @ Tue, 30 Jun 2020 02:12:37: 17000000 INFO @ Tue, 30 Jun 2020 02:12:41: 14000000 INFO @ Tue, 30 Jun 2020 02:12:42: 22000000 INFO @ Tue, 30 Jun 2020 02:12:45: 18000000 INFO @ Tue, 30 Jun 2020 02:12:49: 15000000 INFO @ Tue, 30 Jun 2020 02:12:50: 23000000 INFO @ Tue, 30 Jun 2020 02:12:53: 19000000 INFO @ Tue, 30 Jun 2020 02:12:56: 16000000 INFO @ Tue, 30 Jun 2020 02:12:59: 24000000 INFO @ Tue, 30 Jun 2020 02:13:01: 20000000 INFO @ Tue, 30 Jun 2020 02:13:04: 17000000 INFO @ Tue, 30 Jun 2020 02:13:07: 25000000 INFO @ Tue, 30 Jun 2020 02:13:09: 21000000 INFO @ Tue, 30 Jun 2020 02:13:12: 18000000 INFO @ Tue, 30 Jun 2020 02:13:16: 26000000 INFO @ Tue, 30 Jun 2020 02:13:18: 22000000 INFO @ Tue, 30 Jun 2020 02:13:21: 19000000 INFO @ Tue, 30 Jun 2020 02:13:24: 27000000 INFO @ Tue, 30 Jun 2020 02:13:26: 23000000 INFO @ Tue, 30 Jun 2020 02:13:30: 20000000 INFO @ Tue, 30 Jun 2020 02:13:32: 28000000 INFO @ Tue, 30 Jun 2020 02:13:34: 24000000 INFO @ Tue, 30 Jun 2020 02:13:39: 21000000 INFO @ Tue, 30 Jun 2020 02:13:41: 29000000 INFO @ Tue, 30 Jun 2020 02:13:42: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:13:48: 22000000 INFO @ Tue, 30 Jun 2020 02:13:50: 30000000 INFO @ Tue, 30 Jun 2020 02:13:52: 26000000 INFO @ Tue, 30 Jun 2020 02:13:57: 23000000 INFO @ Tue, 30 Jun 2020 02:13:58: 31000000 INFO @ Tue, 30 Jun 2020 02:14:00: #1 tag size is determined as 70 bps INFO @ Tue, 30 Jun 2020 02:14:00: #1 tag size = 70 INFO @ Tue, 30 Jun 2020 02:14:00: #1 total tags in treatment: 31123209 INFO @ Tue, 30 Jun 2020 02:14:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:14:00: #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 02:14:00: 27000000 INFO @ Tue, 30 Jun 2020 02:14:01: #1 tags after filtering in treatment: 31123209 INFO @ Tue, 30 Jun 2020 02:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:14:01: #1 finished! INFO @ Tue, 30 Jun 2020 02:14:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:14:03: #2 number of paired peaks: 123 WARNING @ Tue, 30 Jun 2020 02:14:03: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 30 Jun 2020 02:14:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:14:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:14:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:14:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:14:03: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 02:14:03: #2 alternative fragment length(s) may be 3,66,567,570,573 bps INFO @ Tue, 30 Jun 2020 02:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.05_model.r WARNING @ Tue, 30 Jun 2020 02:14:03: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:14:03: #2 You may need to consider one of the other alternative d(s): 3,66,567,570,573 WARNING @ Tue, 30 Jun 2020 02:14:03: #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 02:14:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:14:05: 24000000 INFO @ Tue, 30 Jun 2020 02:14:08: 28000000 INFO @ Tue, 30 Jun 2020 02:14:15: 25000000 INFO @ Tue, 30 Jun 2020 02:14:17: 29000000 INFO @ Tue, 30 Jun 2020 02:14:25: 26000000 INFO @ Tue, 30 Jun 2020 02:14:25: 30000000 INFO @ Tue, 30 Jun 2020 02:14:34: 31000000 INFO @ Tue, 30 Jun 2020 02:14:34: 27000000 INFO @ Tue, 30 Jun 2020 02:14:35: #1 tag size is determined as 70 bps INFO @ Tue, 30 Jun 2020 02:14:35: #1 tag size = 70 INFO @ Tue, 30 Jun 2020 02:14:35: #1 total tags in treatment: 31123209 INFO @ Tue, 30 Jun 2020 02:14:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:14:35: #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 02:14:36: #1 tags after filtering in treatment: 31123209 INFO @ Tue, 30 Jun 2020 02:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:14:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:14:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:14:38: #2 number of paired peaks: 123 WARNING @ Tue, 30 Jun 2020 02:14:38: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 30 Jun 2020 02:14:38: start model_add_line... INFO @ Tue, 30 Jun 2020 02:14:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:14:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:14:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:14:39: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 02:14:39: #2 alternative fragment length(s) may be 3,66,567,570,573 bps INFO @ Tue, 30 Jun 2020 02:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.10_model.r WARNING @ Tue, 30 Jun 2020 02:14:39: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:14:39: #2 You may need to consider one of the other alternative d(s): 3,66,567,570,573 WARNING @ Tue, 30 Jun 2020 02:14:39: #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 02:14:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:14:44: 28000000 INFO @ Tue, 30 Jun 2020 02:14:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:14:53: 29000000 INFO @ Tue, 30 Jun 2020 02:15:03: 30000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:15:12: 31000000 INFO @ Tue, 30 Jun 2020 02:15:14: #1 tag size is determined as 70 bps INFO @ Tue, 30 Jun 2020 02:15:14: #1 tag size = 70 INFO @ Tue, 30 Jun 2020 02:15:14: #1 total tags in treatment: 31123209 INFO @ Tue, 30 Jun 2020 02:15:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:14: #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 02:15:15: #1 tags after filtering in treatment: 31123209 INFO @ Tue, 30 Jun 2020 02:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:15:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:15:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.05_summits.bed INFO @ Tue, 30 Jun 2020 02:15:15: Done! pass1 - making usageList (580 chroms): 1 millis pass2 - checking and writing primary data (1933 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:15:17: #2 number of paired peaks: 123 WARNING @ Tue, 30 Jun 2020 02:15:17: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:17: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:17: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:17: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:17: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:17: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 02:15:17: #2 alternative fragment length(s) may be 3,66,567,570,573 bps INFO @ Tue, 30 Jun 2020 02:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.20_model.r WARNING @ Tue, 30 Jun 2020 02:15:17: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:17: #2 You may need to consider one of the other alternative d(s): 3,66,567,570,573 WARNING @ Tue, 30 Jun 2020 02:15:17: #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 02:15:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.10_summits.bed INFO @ Tue, 30 Jun 2020 02:15:50: Done! pass1 - making usageList (487 chroms): 1 millis pass2 - checking and writing primary data (1568 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564144/SRX2564144.20_summits.bed INFO @ Tue, 30 Jun 2020 02:16:28: Done! pass1 - making usageList (402 chroms): 2 millis pass2 - checking and writing primary data (1105 records, 4 fields): 24 millis CompletedMACS2peakCalling