Job ID = 6529705 SRX = SRX3981701 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: 00:10:26 40053952 reads; of these: 40053952 (100.00%) were unpaired; of these: 1395079 (3.48%) aligned 0 times 28947225 (72.27%) aligned exactly 1 time 9711648 (24.25%) aligned >1 times 96.52% overall alignment rate Time searching: 00:10:26 Overall time: 00:10:26 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] 5512302 / 38658873 = 0.1426 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 03:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.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 03:02:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:02:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:02:40: 1000000 INFO @ Tue, 30 Jun 2020 03:02:46: 2000000 INFO @ Tue, 30 Jun 2020 03:02:52: 3000000 INFO @ Tue, 30 Jun 2020 03:02:58: 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 03:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.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 03:03:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:04: 5000000 INFO @ Tue, 30 Jun 2020 03:03:10: 1000000 INFO @ Tue, 30 Jun 2020 03:03:11: 6000000 INFO @ Tue, 30 Jun 2020 03:03:17: 2000000 INFO @ Tue, 30 Jun 2020 03:03:18: 7000000 INFO @ Tue, 30 Jun 2020 03:03:24: 3000000 INFO @ Tue, 30 Jun 2020 03:03:24: 8000000 INFO @ Tue, 30 Jun 2020 03:03:30: 4000000 INFO @ Tue, 30 Jun 2020 03:03:31: 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 03:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.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 03:03:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:37: 5000000 INFO @ Tue, 30 Jun 2020 03:03:38: 10000000 INFO @ Tue, 30 Jun 2020 03:03:42: 1000000 INFO @ Tue, 30 Jun 2020 03:03:44: 6000000 INFO @ Tue, 30 Jun 2020 03:03:46: 11000000 INFO @ Tue, 30 Jun 2020 03:03:49: 2000000 INFO @ Tue, 30 Jun 2020 03:03:51: 7000000 INFO @ Tue, 30 Jun 2020 03:03:54: 12000000 INFO @ Tue, 30 Jun 2020 03:03:57: 3000000 INFO @ Tue, 30 Jun 2020 03:03:58: 8000000 INFO @ Tue, 30 Jun 2020 03:04:02: 13000000 INFO @ Tue, 30 Jun 2020 03:04:04: 9000000 INFO @ Tue, 30 Jun 2020 03:04:05: 4000000 INFO @ Tue, 30 Jun 2020 03:04:09: 14000000 INFO @ Tue, 30 Jun 2020 03:04:11: 10000000 INFO @ Tue, 30 Jun 2020 03:04:13: 5000000 INFO @ Tue, 30 Jun 2020 03:04:17: 15000000 INFO @ Tue, 30 Jun 2020 03:04:18: 11000000 INFO @ Tue, 30 Jun 2020 03:04:21: 6000000 INFO @ Tue, 30 Jun 2020 03:04:25: 12000000 INFO @ Tue, 30 Jun 2020 03:04:25: 16000000 INFO @ Tue, 30 Jun 2020 03:04:28: 7000000 INFO @ Tue, 30 Jun 2020 03:04:31: 13000000 INFO @ Tue, 30 Jun 2020 03:04:33: 17000000 INFO @ Tue, 30 Jun 2020 03:04:37: 8000000 INFO @ Tue, 30 Jun 2020 03:04:38: 14000000 INFO @ Tue, 30 Jun 2020 03:04:41: 18000000 INFO @ Tue, 30 Jun 2020 03:04:44: 15000000 INFO @ Tue, 30 Jun 2020 03:04:45: 9000000 INFO @ Tue, 30 Jun 2020 03:04:50: 19000000 INFO @ Tue, 30 Jun 2020 03:04:51: 16000000 INFO @ Tue, 30 Jun 2020 03:04:54: 10000000 INFO @ Tue, 30 Jun 2020 03:04:58: 17000000 INFO @ Tue, 30 Jun 2020 03:04:59: 20000000 INFO @ Tue, 30 Jun 2020 03:05:03: 11000000 INFO @ Tue, 30 Jun 2020 03:05:04: 18000000 INFO @ Tue, 30 Jun 2020 03:05:08: 21000000 INFO @ Tue, 30 Jun 2020 03:05:11: 19000000 INFO @ Tue, 30 Jun 2020 03:05:13: 12000000 INFO @ Tue, 30 Jun 2020 03:05:18: 20000000 INFO @ Tue, 30 Jun 2020 03:05:18: 22000000 INFO @ Tue, 30 Jun 2020 03:05:22: 13000000 INFO @ Tue, 30 Jun 2020 03:05:24: 21000000 INFO @ Tue, 30 Jun 2020 03:05:27: 23000000 INFO @ Tue, 30 Jun 2020 03:05:31: 22000000 INFO @ Tue, 30 Jun 2020 03:05:31: 14000000 INFO @ Tue, 30 Jun 2020 03:05:36: 24000000 INFO @ Tue, 30 Jun 2020 03:05:39: 23000000 INFO @ Tue, 30 Jun 2020 03:05:41: 15000000 INFO @ Tue, 30 Jun 2020 03:05:45: 25000000 INFO @ Tue, 30 Jun 2020 03:05:46: 24000000 INFO @ Tue, 30 Jun 2020 03:05:50: 16000000 INFO @ Tue, 30 Jun 2020 03:05:54: 25000000 INFO @ Tue, 30 Jun 2020 03:05:55: 26000000 INFO @ Tue, 30 Jun 2020 03:05:59: 17000000 INFO @ Tue, 30 Jun 2020 03:06:02: 26000000 INFO @ Tue, 30 Jun 2020 03:06:04: 27000000 INFO @ Tue, 30 Jun 2020 03:06:08: 18000000 INFO @ Tue, 30 Jun 2020 03:06:10: 27000000 INFO @ Tue, 30 Jun 2020 03:06:13: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:06:17: 19000000 INFO @ Tue, 30 Jun 2020 03:06:18: 28000000 INFO @ Tue, 30 Jun 2020 03:06:23: 29000000 INFO @ Tue, 30 Jun 2020 03:06:27: 29000000 INFO @ Tue, 30 Jun 2020 03:06:27: 20000000 INFO @ Tue, 30 Jun 2020 03:06:33: 30000000 INFO @ Tue, 30 Jun 2020 03:06:36: 30000000 INFO @ Tue, 30 Jun 2020 03:06:37: 21000000 INFO @ Tue, 30 Jun 2020 03:06:42: 31000000 INFO @ Tue, 30 Jun 2020 03:06:45: 31000000 INFO @ Tue, 30 Jun 2020 03:06:46: 22000000 INFO @ Tue, 30 Jun 2020 03:06:51: 32000000 INFO @ Tue, 30 Jun 2020 03:06:54: 32000000 INFO @ Tue, 30 Jun 2020 03:06:55: 23000000 INFO @ Tue, 30 Jun 2020 03:07:01: 33000000 INFO @ Tue, 30 Jun 2020 03:07:02: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:07:02: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:07:02: #1 total tags in treatment: 33146571 INFO @ Tue, 30 Jun 2020 03:07:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:07:02: #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 03:07:03: 33000000 INFO @ Tue, 30 Jun 2020 03:07:03: #1 tags after filtering in treatment: 33146519 INFO @ Tue, 30 Jun 2020 03:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:07:03: #1 finished! INFO @ Tue, 30 Jun 2020 03:07:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:07:04: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:07:04: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:07:04: #1 total tags in treatment: 33146571 INFO @ Tue, 30 Jun 2020 03:07:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:07:04: #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 03:07:05: 24000000 INFO @ Tue, 30 Jun 2020 03:07:05: #1 tags after filtering in treatment: 33146519 INFO @ Tue, 30 Jun 2020 03:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:07:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:07:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:07:05: #2 number of paired peaks: 148 WARNING @ Tue, 30 Jun 2020 03:07:05: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 30 Jun 2020 03:07:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:07:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:07:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:07:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:07:06: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 03:07:06: #2 alternative fragment length(s) may be 1,47,487,503,528 bps INFO @ Tue, 30 Jun 2020 03:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.05_model.r WARNING @ Tue, 30 Jun 2020 03:07:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:07:06: #2 You may need to consider one of the other alternative d(s): 1,47,487,503,528 WARNING @ Tue, 30 Jun 2020 03:07:06: #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 03:07:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:07:07: #2 number of paired peaks: 148 WARNING @ Tue, 30 Jun 2020 03:07:07: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 30 Jun 2020 03:07:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:07:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:07:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:07:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:07:07: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 03:07:07: #2 alternative fragment length(s) may be 1,47,487,503,528 bps INFO @ Tue, 30 Jun 2020 03:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.10_model.r WARNING @ Tue, 30 Jun 2020 03:07:07: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:07:07: #2 You may need to consider one of the other alternative d(s): 1,47,487,503,528 WARNING @ Tue, 30 Jun 2020 03:07:07: #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 03:07:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:07:14: 25000000 INFO @ Tue, 30 Jun 2020 03:07:24: 26000000 INFO @ Tue, 30 Jun 2020 03:07:33: 27000000 INFO @ Tue, 30 Jun 2020 03:07:41: 28000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:07:50: 29000000 INFO @ Tue, 30 Jun 2020 03:07:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:59: 30000000 INFO @ Tue, 30 Jun 2020 03:08:07: 31000000 INFO @ Tue, 30 Jun 2020 03:08:16: 32000000 INFO @ Tue, 30 Jun 2020 03:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.05_summits.bed INFO @ Tue, 30 Jun 2020 03:08:21: Done! pass1 - making usageList (620 chroms): 2 millis pass2 - checking and writing primary data (3137 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.10_summits.bed INFO @ Tue, 30 Jun 2020 03:08:24: Done! INFO @ Tue, 30 Jun 2020 03:08:24: 33000000 pass1 - making usageList (488 chroms): 1 millis pass2 - checking and writing primary data (1737 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:08:25: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:08:25: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:08:25: #1 total tags in treatment: 33146571 INFO @ Tue, 30 Jun 2020 03:08:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:08:25: #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 03:08:27: #1 tags after filtering in treatment: 33146519 INFO @ Tue, 30 Jun 2020 03:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:08:27: #1 finished! INFO @ Tue, 30 Jun 2020 03:08:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:08:29: #2 number of paired peaks: 148 WARNING @ Tue, 30 Jun 2020 03:08:29: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 30 Jun 2020 03:08:29: start model_add_line... INFO @ Tue, 30 Jun 2020 03:08:29: start X-correlation... INFO @ Tue, 30 Jun 2020 03:08:29: end of X-cor INFO @ Tue, 30 Jun 2020 03:08:29: #2 finished! INFO @ Tue, 30 Jun 2020 03:08:29: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 03:08:29: #2 alternative fragment length(s) may be 1,47,487,503,528 bps INFO @ Tue, 30 Jun 2020 03:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.20_model.r WARNING @ Tue, 30 Jun 2020 03:08:29: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:08:29: #2 You may need to consider one of the other alternative d(s): 1,47,487,503,528 WARNING @ Tue, 30 Jun 2020 03:08:29: #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 03:08:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:09:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:09:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:09:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:09:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981701/SRX3981701.20_summits.bed INFO @ Tue, 30 Jun 2020 03:09:45: Done! pass1 - making usageList (233 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 14 millis CompletedMACS2peakCalling