Job ID = 6529410 SRX = SRX2564142 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:47 46769695 reads; of these: 46769695 (100.00%) were unpaired; of these: 5338942 (11.42%) aligned 0 times 32379751 (69.23%) aligned exactly 1 time 9051002 (19.35%) aligned >1 times 88.58% overall alignment rate Time searching: 00:18:48 Overall time: 00:18:48 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] 6384667 / 41430753 = 0.1541 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 02:40:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.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 02:40:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:18: 1000000 INFO @ Tue, 30 Jun 2020 02:40:26: 2000000 INFO @ Tue, 30 Jun 2020 02:40:34: 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 02:40:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.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 02:40:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:43: 4000000 INFO @ Tue, 30 Jun 2020 02:40:49: 1000000 INFO @ Tue, 30 Jun 2020 02:40:51: 5000000 INFO @ Tue, 30 Jun 2020 02:40:58: 2000000 INFO @ Tue, 30 Jun 2020 02:41:00: 6000000 INFO @ Tue, 30 Jun 2020 02:41:06: 3000000 INFO @ Tue, 30 Jun 2020 02:41:08: 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 02:41:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.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 02:41:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:15: 4000000 INFO @ Tue, 30 Jun 2020 02:41:17: 8000000 INFO @ Tue, 30 Jun 2020 02:41:19: 1000000 INFO @ Tue, 30 Jun 2020 02:41:24: 5000000 INFO @ Tue, 30 Jun 2020 02:41:26: 9000000 INFO @ Tue, 30 Jun 2020 02:41:28: 2000000 INFO @ Tue, 30 Jun 2020 02:41:32: 6000000 INFO @ Tue, 30 Jun 2020 02:41:34: 10000000 INFO @ Tue, 30 Jun 2020 02:41:36: 3000000 INFO @ Tue, 30 Jun 2020 02:41:41: 7000000 INFO @ Tue, 30 Jun 2020 02:41:43: 11000000 INFO @ Tue, 30 Jun 2020 02:41:46: 4000000 INFO @ Tue, 30 Jun 2020 02:41:50: 8000000 INFO @ Tue, 30 Jun 2020 02:41:52: 12000000 INFO @ Tue, 30 Jun 2020 02:41:54: 5000000 INFO @ Tue, 30 Jun 2020 02:41:59: 9000000 INFO @ Tue, 30 Jun 2020 02:42:01: 13000000 INFO @ Tue, 30 Jun 2020 02:42:03: 6000000 INFO @ Tue, 30 Jun 2020 02:42:07: 10000000 INFO @ Tue, 30 Jun 2020 02:42:09: 14000000 INFO @ Tue, 30 Jun 2020 02:42:12: 7000000 INFO @ Tue, 30 Jun 2020 02:42:16: 11000000 INFO @ Tue, 30 Jun 2020 02:42:18: 15000000 INFO @ Tue, 30 Jun 2020 02:42:22: 8000000 INFO @ Tue, 30 Jun 2020 02:42:25: 12000000 INFO @ Tue, 30 Jun 2020 02:42:27: 16000000 INFO @ Tue, 30 Jun 2020 02:42:31: 9000000 INFO @ Tue, 30 Jun 2020 02:42:33: 13000000 INFO @ Tue, 30 Jun 2020 02:42:35: 17000000 INFO @ Tue, 30 Jun 2020 02:42:39: 10000000 INFO @ Tue, 30 Jun 2020 02:42:42: 14000000 INFO @ Tue, 30 Jun 2020 02:42:44: 18000000 INFO @ Tue, 30 Jun 2020 02:42:48: 11000000 INFO @ Tue, 30 Jun 2020 02:42:51: 15000000 INFO @ Tue, 30 Jun 2020 02:42:53: 19000000 INFO @ Tue, 30 Jun 2020 02:42:57: 12000000 INFO @ Tue, 30 Jun 2020 02:42:59: 16000000 INFO @ Tue, 30 Jun 2020 02:43:02: 20000000 INFO @ Tue, 30 Jun 2020 02:43:06: 13000000 INFO @ Tue, 30 Jun 2020 02:43:08: 17000000 INFO @ Tue, 30 Jun 2020 02:43:11: 21000000 INFO @ Tue, 30 Jun 2020 02:43:15: 14000000 INFO @ Tue, 30 Jun 2020 02:43:17: 18000000 INFO @ Tue, 30 Jun 2020 02:43:20: 22000000 INFO @ Tue, 30 Jun 2020 02:43:24: 15000000 INFO @ Tue, 30 Jun 2020 02:43:26: 19000000 INFO @ Tue, 30 Jun 2020 02:43:29: 23000000 INFO @ Tue, 30 Jun 2020 02:43:33: 16000000 INFO @ Tue, 30 Jun 2020 02:43:36: 20000000 INFO @ Tue, 30 Jun 2020 02:43:38: 24000000 INFO @ Tue, 30 Jun 2020 02:43:42: 17000000 INFO @ Tue, 30 Jun 2020 02:43:45: 21000000 INFO @ Tue, 30 Jun 2020 02:43:47: 25000000 INFO @ Tue, 30 Jun 2020 02:43:51: 18000000 INFO @ Tue, 30 Jun 2020 02:43:54: 22000000 INFO @ Tue, 30 Jun 2020 02:43:56: 26000000 INFO @ Tue, 30 Jun 2020 02:44:00: 19000000 INFO @ Tue, 30 Jun 2020 02:44:03: 23000000 INFO @ Tue, 30 Jun 2020 02:44:05: 27000000 INFO @ Tue, 30 Jun 2020 02:44:09: 20000000 INFO @ Tue, 30 Jun 2020 02:44:11: 24000000 INFO @ Tue, 30 Jun 2020 02:44:15: 28000000 INFO @ Tue, 30 Jun 2020 02:44:18: 21000000 INFO @ Tue, 30 Jun 2020 02:44:20: 25000000 INFO @ Tue, 30 Jun 2020 02:44:24: 29000000 INFO @ Tue, 30 Jun 2020 02:44:26: 22000000 INFO @ Tue, 30 Jun 2020 02:44:29: 26000000 INFO @ Tue, 30 Jun 2020 02:44:33: 30000000 INFO @ Tue, 30 Jun 2020 02:44:35: 23000000 INFO @ Tue, 30 Jun 2020 02:44:38: 27000000 INFO @ Tue, 30 Jun 2020 02:44:43: 31000000 INFO @ Tue, 30 Jun 2020 02:44:44: 24000000 INFO @ Tue, 30 Jun 2020 02:44:47: 28000000 INFO @ Tue, 30 Jun 2020 02:44:52: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:44:53: 25000000 INFO @ Tue, 30 Jun 2020 02:44:57: 29000000 INFO @ Tue, 30 Jun 2020 02:45:01: 33000000 INFO @ Tue, 30 Jun 2020 02:45:02: 26000000 INFO @ Tue, 30 Jun 2020 02:45:06: 30000000 INFO @ Tue, 30 Jun 2020 02:45:10: 34000000 INFO @ Tue, 30 Jun 2020 02:45:11: 27000000 INFO @ Tue, 30 Jun 2020 02:45:15: 31000000 INFO @ Tue, 30 Jun 2020 02:45:19: 35000000 INFO @ Tue, 30 Jun 2020 02:45:19: 28000000 INFO @ Tue, 30 Jun 2020 02:45:20: #1 tag size is determined as 73 bps INFO @ Tue, 30 Jun 2020 02:45:20: #1 tag size = 73 INFO @ Tue, 30 Jun 2020 02:45:20: #1 total tags in treatment: 35046086 INFO @ Tue, 30 Jun 2020 02:45:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:45:20: #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 02:45:21: #1 tags after filtering in treatment: 35046086 INFO @ Tue, 30 Jun 2020 02:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:45:21: #1 finished! INFO @ Tue, 30 Jun 2020 02:45:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:45:23: #2 number of paired peaks: 155 WARNING @ Tue, 30 Jun 2020 02:45:23: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 30 Jun 2020 02:45:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:45:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:45:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:45:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:45:23: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:45:23: #2 alternative fragment length(s) may be 2,39,51,53 bps INFO @ Tue, 30 Jun 2020 02:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.05_model.r WARNING @ Tue, 30 Jun 2020 02:45:23: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:45:23: #2 You may need to consider one of the other alternative d(s): 2,39,51,53 WARNING @ Tue, 30 Jun 2020 02:45:23: #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 02:45:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:45:24: 32000000 INFO @ Tue, 30 Jun 2020 02:45:28: 29000000 INFO @ Tue, 30 Jun 2020 02:45:32: 33000000 INFO @ Tue, 30 Jun 2020 02:45:37: 30000000 INFO @ Tue, 30 Jun 2020 02:45:41: 34000000 INFO @ Tue, 30 Jun 2020 02:45:45: 31000000 INFO @ Tue, 30 Jun 2020 02:45:49: 35000000 INFO @ Tue, 30 Jun 2020 02:45:50: #1 tag size is determined as 73 bps INFO @ Tue, 30 Jun 2020 02:45:50: #1 tag size = 73 INFO @ Tue, 30 Jun 2020 02:45:50: #1 total tags in treatment: 35046086 INFO @ Tue, 30 Jun 2020 02:45:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:45:50: #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 02:45:51: #1 tags after filtering in treatment: 35046086 INFO @ Tue, 30 Jun 2020 02:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:45:51: #1 finished! INFO @ Tue, 30 Jun 2020 02:45:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:45:53: 32000000 INFO @ Tue, 30 Jun 2020 02:45:54: #2 number of paired peaks: 155 WARNING @ Tue, 30 Jun 2020 02:45:54: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 30 Jun 2020 02:45:54: start model_add_line... INFO @ Tue, 30 Jun 2020 02:45:54: start X-correlation... INFO @ Tue, 30 Jun 2020 02:45:54: end of X-cor INFO @ Tue, 30 Jun 2020 02:45:54: #2 finished! INFO @ Tue, 30 Jun 2020 02:45:54: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:45:54: #2 alternative fragment length(s) may be 2,39,51,53 bps INFO @ Tue, 30 Jun 2020 02:45:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.10_model.r WARNING @ Tue, 30 Jun 2020 02:45:54: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:45:54: #2 You may need to consider one of the other alternative d(s): 2,39,51,53 WARNING @ Tue, 30 Jun 2020 02:45:54: #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 02:45:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:45:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:46:01: 33000000 INFO @ Tue, 30 Jun 2020 02:46:09: 34000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:46:18: 35000000 INFO @ Tue, 30 Jun 2020 02:46:19: #1 tag size is determined as 73 bps INFO @ Tue, 30 Jun 2020 02:46:19: #1 tag size = 73 INFO @ Tue, 30 Jun 2020 02:46:19: #1 total tags in treatment: 35046086 INFO @ Tue, 30 Jun 2020 02:46:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:46:19: #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 02:46:20: #1 tags after filtering in treatment: 35046086 INFO @ Tue, 30 Jun 2020 02:46:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:46:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:46:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:46:22: #2 number of paired peaks: 155 WARNING @ Tue, 30 Jun 2020 02:46:22: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 30 Jun 2020 02:46:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:46:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:46:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:46:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:46:22: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:46:22: #2 alternative fragment length(s) may be 2,39,51,53 bps INFO @ Tue, 30 Jun 2020 02:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.20_model.r WARNING @ Tue, 30 Jun 2020 02:46:22: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:46:22: #2 You may need to consider one of the other alternative d(s): 2,39,51,53 WARNING @ Tue, 30 Jun 2020 02:46:22: #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 02:46:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:46:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.05_summits.bed INFO @ Tue, 30 Jun 2020 02:46:56: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (1885 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:46:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:47:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.10_summits.bed INFO @ Tue, 30 Jun 2020 02:47:27: Done! pass1 - making usageList (484 chroms): 2 millis pass2 - checking and writing primary data (1563 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:47:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:47:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:47:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564142/SRX2564142.20_summits.bed INFO @ Tue, 30 Jun 2020 02:47:55: Done! pass1 - making usageList (384 chroms): 1 millis pass2 - checking and writing primary data (996 records, 4 fields): 12 millis CompletedMACS2peakCalling