Job ID = 6529440 SRX = SRX2734370 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: 00:06:56 32127329 reads; of these: 32127329 (100.00%) were unpaired; of these: 1669043 (5.20%) aligned 0 times 26495959 (82.47%) aligned exactly 1 time 3962327 (12.33%) aligned >1 times 94.80% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 3818650 / 30458286 = 0.1254 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 02:01:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.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 02:01:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:55: 1000000 INFO @ Tue, 30 Jun 2020 02:02:02: 2000000 INFO @ Tue, 30 Jun 2020 02:02:08: 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 02:02:16: 4000000 INFO @ Tue, 30 Jun 2020 02:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.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 02:02:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:23: 5000000 INFO @ Tue, 30 Jun 2020 02:02:25: 1000000 INFO @ Tue, 30 Jun 2020 02:02:30: 6000000 INFO @ Tue, 30 Jun 2020 02:02:33: 2000000 INFO @ Tue, 30 Jun 2020 02:02:38: 7000000 INFO @ Tue, 30 Jun 2020 02:02:41: 3000000 INFO @ Tue, 30 Jun 2020 02:02:45: 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 02:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.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 02:02:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:48: 4000000 INFO @ Tue, 30 Jun 2020 02:02:52: 9000000 INFO @ Tue, 30 Jun 2020 02:02:55: 1000000 INFO @ Tue, 30 Jun 2020 02:02:56: 5000000 INFO @ Tue, 30 Jun 2020 02:03:00: 10000000 INFO @ Tue, 30 Jun 2020 02:03:03: 2000000 INFO @ Tue, 30 Jun 2020 02:03:03: 6000000 INFO @ Tue, 30 Jun 2020 02:03:07: 11000000 INFO @ Tue, 30 Jun 2020 02:03:11: 3000000 INFO @ Tue, 30 Jun 2020 02:03:11: 7000000 INFO @ Tue, 30 Jun 2020 02:03:15: 12000000 INFO @ Tue, 30 Jun 2020 02:03:18: 4000000 INFO @ Tue, 30 Jun 2020 02:03:18: 8000000 INFO @ Tue, 30 Jun 2020 02:03:22: 13000000 INFO @ Tue, 30 Jun 2020 02:03:26: 5000000 INFO @ Tue, 30 Jun 2020 02:03:26: 9000000 INFO @ Tue, 30 Jun 2020 02:03:30: 14000000 INFO @ Tue, 30 Jun 2020 02:03:33: 6000000 INFO @ Tue, 30 Jun 2020 02:03:34: 10000000 INFO @ Tue, 30 Jun 2020 02:03:37: 15000000 INFO @ Tue, 30 Jun 2020 02:03:41: 7000000 INFO @ Tue, 30 Jun 2020 02:03:42: 11000000 INFO @ Tue, 30 Jun 2020 02:03:45: 16000000 INFO @ Tue, 30 Jun 2020 02:03:49: 8000000 INFO @ Tue, 30 Jun 2020 02:03:49: 12000000 INFO @ Tue, 30 Jun 2020 02:03:53: 17000000 INFO @ Tue, 30 Jun 2020 02:03:56: 9000000 INFO @ Tue, 30 Jun 2020 02:03:57: 13000000 INFO @ Tue, 30 Jun 2020 02:04:00: 18000000 INFO @ Tue, 30 Jun 2020 02:04:04: 10000000 INFO @ Tue, 30 Jun 2020 02:04:05: 14000000 INFO @ Tue, 30 Jun 2020 02:04:08: 19000000 INFO @ Tue, 30 Jun 2020 02:04:12: 11000000 INFO @ Tue, 30 Jun 2020 02:04:13: 15000000 INFO @ Tue, 30 Jun 2020 02:04:15: 20000000 INFO @ Tue, 30 Jun 2020 02:04:19: 12000000 INFO @ Tue, 30 Jun 2020 02:04:20: 16000000 INFO @ Tue, 30 Jun 2020 02:04:23: 21000000 INFO @ Tue, 30 Jun 2020 02:04:27: 13000000 INFO @ Tue, 30 Jun 2020 02:04:28: 17000000 INFO @ Tue, 30 Jun 2020 02:04:32: 22000000 INFO @ Tue, 30 Jun 2020 02:04:35: 14000000 INFO @ Tue, 30 Jun 2020 02:04:36: 18000000 INFO @ Tue, 30 Jun 2020 02:04:39: 23000000 INFO @ Tue, 30 Jun 2020 02:04:42: 15000000 INFO @ Tue, 30 Jun 2020 02:04:43: 19000000 INFO @ Tue, 30 Jun 2020 02:04:47: 24000000 INFO @ Tue, 30 Jun 2020 02:04:50: 16000000 INFO @ Tue, 30 Jun 2020 02:04:51: 20000000 INFO @ Tue, 30 Jun 2020 02:04:54: 25000000 INFO @ Tue, 30 Jun 2020 02:04:57: 17000000 INFO @ Tue, 30 Jun 2020 02:04:59: 21000000 INFO @ Tue, 30 Jun 2020 02:05:02: 26000000 INFO @ Tue, 30 Jun 2020 02:05:05: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:05:07: 22000000 INFO @ Tue, 30 Jun 2020 02:05:07: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:05:07: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:05:07: #1 total tags in treatment: 26639636 INFO @ Tue, 30 Jun 2020 02:05:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:07: #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 02:05:08: #1 tags after filtering in treatment: 26639578 INFO @ Tue, 30 Jun 2020 02:05:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:10: #2 number of paired peaks: 137 WARNING @ Tue, 30 Jun 2020 02:05:10: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:10: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:05:10: #2 alternative fragment length(s) may be 1,49,65,118,144,573,588 bps INFO @ Tue, 30 Jun 2020 02:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.05_model.r WARNING @ Tue, 30 Jun 2020 02:05:10: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:05:10: #2 You may need to consider one of the other alternative d(s): 1,49,65,118,144,573,588 WARNING @ Tue, 30 Jun 2020 02:05:10: #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 02:05:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:13: 19000000 INFO @ Tue, 30 Jun 2020 02:05:15: 23000000 INFO @ Tue, 30 Jun 2020 02:05:20: 20000000 INFO @ Tue, 30 Jun 2020 02:05:23: 24000000 INFO @ Tue, 30 Jun 2020 02:05:28: 21000000 INFO @ Tue, 30 Jun 2020 02:05:30: 25000000 INFO @ Tue, 30 Jun 2020 02:05:36: 22000000 INFO @ Tue, 30 Jun 2020 02:05:38: 26000000 INFO @ Tue, 30 Jun 2020 02:05:43: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:05:43: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:05:43: #1 total tags in treatment: 26639636 INFO @ Tue, 30 Jun 2020 02:05:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:43: #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 02:05:43: 23000000 INFO @ Tue, 30 Jun 2020 02:05:44: #1 tags after filtering in treatment: 26639578 INFO @ Tue, 30 Jun 2020 02:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:46: #2 number of paired peaks: 137 WARNING @ Tue, 30 Jun 2020 02:05:46: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:46: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:05:46: #2 alternative fragment length(s) may be 1,49,65,118,144,573,588 bps INFO @ Tue, 30 Jun 2020 02:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.10_model.r WARNING @ Tue, 30 Jun 2020 02:05:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:05:46: #2 You may need to consider one of the other alternative d(s): 1,49,65,118,144,573,588 WARNING @ Tue, 30 Jun 2020 02:05:46: #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 02:05:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:51: 24000000 INFO @ Tue, 30 Jun 2020 02:05:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:58: 25000000 INFO @ Tue, 30 Jun 2020 02:06:05: 26000000 INFO @ Tue, 30 Jun 2020 02:06:10: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:10: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:10: #1 total tags in treatment: 26639636 INFO @ Tue, 30 Jun 2020 02:06:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:10: #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 02:06:11: #1 tags after filtering in treatment: 26639578 INFO @ Tue, 30 Jun 2020 02:06:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:11: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:13: #2 number of paired peaks: 137 WARNING @ Tue, 30 Jun 2020 02:06:13: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:13: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:06:13: #2 alternative fragment length(s) may be 1,49,65,118,144,573,588 bps INFO @ Tue, 30 Jun 2020 02:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.20_model.r WARNING @ Tue, 30 Jun 2020 02:06:13: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:13: #2 You may need to consider one of the other alternative d(s): 1,49,65,118,144,573,588 WARNING @ Tue, 30 Jun 2020 02:06:13: #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 02:06:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.05_summits.bed INFO @ Tue, 30 Jun 2020 02:06:18: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:06:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.10_summits.bed INFO @ Tue, 30 Jun 2020 02:06:54: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:06:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734370/SRX2734370.20_summits.bed INFO @ Tue, 30 Jun 2020 02:07:20: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 6 millis CompletedMACS2peakCalling