Job ID = 6529861 SRX = SRX5287835 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: 00:10:47 25177504 reads; of these: 25177504 (100.00%) were unpaired; of these: 945152 (3.75%) aligned 0 times 18180539 (72.21%) aligned exactly 1 time 6051813 (24.04%) aligned >1 times 96.25% overall alignment rate Time searching: 00:10:47 Overall time: 00:10:47 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 12 files... [bam_rmdupse_core] 3058710 / 24232352 = 0.1262 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 03:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.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 03:13:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:05: 1000000 INFO @ Tue, 30 Jun 2020 03:14:12: 2000000 INFO @ Tue, 30 Jun 2020 03:14:18: 3000000 INFO @ Tue, 30 Jun 2020 03:14:24: 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 03:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.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 03:14:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:31: 5000000 INFO @ Tue, 30 Jun 2020 03:14:34: 1000000 INFO @ Tue, 30 Jun 2020 03:14:37: 6000000 INFO @ Tue, 30 Jun 2020 03:14:41: 2000000 INFO @ Tue, 30 Jun 2020 03:14:43: 7000000 INFO @ Tue, 30 Jun 2020 03:14:47: 3000000 INFO @ Tue, 30 Jun 2020 03:14:50: 8000000 INFO @ Tue, 30 Jun 2020 03:14:53: 4000000 INFO @ Tue, 30 Jun 2020 03:14:56: 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 03:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.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 03:14:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:59: 5000000 INFO @ Tue, 30 Jun 2020 03:15:03: 10000000 INFO @ Tue, 30 Jun 2020 03:15:05: 6000000 INFO @ Tue, 30 Jun 2020 03:15:05: 1000000 INFO @ Tue, 30 Jun 2020 03:15:09: 11000000 INFO @ Tue, 30 Jun 2020 03:15:11: 7000000 INFO @ Tue, 30 Jun 2020 03:15:12: 2000000 INFO @ Tue, 30 Jun 2020 03:15:15: 12000000 INFO @ Tue, 30 Jun 2020 03:15:18: 8000000 INFO @ Tue, 30 Jun 2020 03:15:18: 3000000 INFO @ Tue, 30 Jun 2020 03:15:22: 13000000 INFO @ Tue, 30 Jun 2020 03:15:24: 9000000 INFO @ Tue, 30 Jun 2020 03:15:25: 4000000 INFO @ Tue, 30 Jun 2020 03:15:28: 14000000 INFO @ Tue, 30 Jun 2020 03:15:30: 10000000 INFO @ Tue, 30 Jun 2020 03:15:31: 5000000 INFO @ Tue, 30 Jun 2020 03:15:34: 15000000 INFO @ Tue, 30 Jun 2020 03:15:36: 11000000 INFO @ Tue, 30 Jun 2020 03:15:38: 6000000 INFO @ Tue, 30 Jun 2020 03:15:40: 16000000 INFO @ Tue, 30 Jun 2020 03:15:43: 12000000 INFO @ Tue, 30 Jun 2020 03:15:45: 7000000 INFO @ Tue, 30 Jun 2020 03:15:47: 17000000 INFO @ Tue, 30 Jun 2020 03:15:49: 13000000 INFO @ Tue, 30 Jun 2020 03:15:52: 8000000 INFO @ Tue, 30 Jun 2020 03:15:53: 18000000 INFO @ Tue, 30 Jun 2020 03:15:56: 14000000 INFO @ Tue, 30 Jun 2020 03:15:59: 9000000 INFO @ Tue, 30 Jun 2020 03:16:00: 19000000 INFO @ Tue, 30 Jun 2020 03:16:02: 15000000 INFO @ Tue, 30 Jun 2020 03:16:06: 10000000 INFO @ Tue, 30 Jun 2020 03:16:06: 20000000 INFO @ Tue, 30 Jun 2020 03:16:08: 16000000 INFO @ Tue, 30 Jun 2020 03:16:12: 11000000 INFO @ Tue, 30 Jun 2020 03:16:13: 21000000 INFO @ Tue, 30 Jun 2020 03:16:15: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:16:15: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:16:15: #1 total tags in treatment: 21173642 INFO @ Tue, 30 Jun 2020 03:16:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:15: #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 03:16:15: 17000000 INFO @ Tue, 30 Jun 2020 03:16:15: #1 tags after filtering in treatment: 21173642 INFO @ Tue, 30 Jun 2020 03:16:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:15: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:17: #2 number of paired peaks: 429 WARNING @ Tue, 30 Jun 2020 03:16:17: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:17: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:17: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:17: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:17: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:17: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:16:17: #2 alternative fragment length(s) may be 3,45,53 bps INFO @ Tue, 30 Jun 2020 03:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.05_model.r WARNING @ Tue, 30 Jun 2020 03:16:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:17: #2 You may need to consider one of the other alternative d(s): 3,45,53 WARNING @ Tue, 30 Jun 2020 03:16:17: #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 03:16:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:19: 12000000 INFO @ Tue, 30 Jun 2020 03:16:22: 18000000 INFO @ Tue, 30 Jun 2020 03:16:26: 13000000 INFO @ Tue, 30 Jun 2020 03:16:28: 19000000 INFO @ Tue, 30 Jun 2020 03:16:32: 14000000 INFO @ Tue, 30 Jun 2020 03:16:34: 20000000 INFO @ Tue, 30 Jun 2020 03:16:39: 15000000 INFO @ Tue, 30 Jun 2020 03:16:41: 21000000 INFO @ Tue, 30 Jun 2020 03:16:42: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:16:42: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:16:42: #1 total tags in treatment: 21173642 INFO @ Tue, 30 Jun 2020 03:16:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:42: #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 03:16:43: #1 tags after filtering in treatment: 21173642 INFO @ Tue, 30 Jun 2020 03:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:43: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:45: #2 number of paired peaks: 429 WARNING @ Tue, 30 Jun 2020 03:16:45: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:45: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:45: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:45: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:45: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:45: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:16:45: #2 alternative fragment length(s) may be 3,45,53 bps INFO @ Tue, 30 Jun 2020 03:16:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.10_model.r WARNING @ Tue, 30 Jun 2020 03:16:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:45: #2 You may need to consider one of the other alternative d(s): 3,45,53 WARNING @ Tue, 30 Jun 2020 03:16:45: #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 03:16:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:46: 16000000 INFO @ Tue, 30 Jun 2020 03:16:53: 17000000 INFO @ Tue, 30 Jun 2020 03:17:00: 18000000 INFO @ Tue, 30 Jun 2020 03:17:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:06: 19000000 INFO @ Tue, 30 Jun 2020 03:17:13: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:17:20: 21000000 INFO @ Tue, 30 Jun 2020 03:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.05_summits.bed INFO @ Tue, 30 Jun 2020 03:17:21: Done! pass1 - making usageList (687 chroms): 1 millis pass2 - checking and writing primary data (2388 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:17:21: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:17:21: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:17:21: #1 total tags in treatment: 21173642 INFO @ Tue, 30 Jun 2020 03:17:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:21: #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 03:17:22: #1 tags after filtering in treatment: 21173642 INFO @ Tue, 30 Jun 2020 03:17:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:22: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:24: #2 number of paired peaks: 429 WARNING @ Tue, 30 Jun 2020 03:17:24: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:24: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:24: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:24: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:24: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:24: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:17:24: #2 alternative fragment length(s) may be 3,45,53 bps INFO @ Tue, 30 Jun 2020 03:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.20_model.r WARNING @ Tue, 30 Jun 2020 03:17:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:24: #2 You may need to consider one of the other alternative d(s): 3,45,53 WARNING @ Tue, 30 Jun 2020 03:17:24: #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 03:17:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:17:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.10_summits.bed INFO @ Tue, 30 Jun 2020 03:17:50: Done! pass1 - making usageList (566 chroms): 2 millis pass2 - checking and writing primary data (1730 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:18:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287835/SRX5287835.20_summits.bed INFO @ Tue, 30 Jun 2020 03:18:28: Done! pass1 - making usageList (421 chroms): 1 millis pass2 - checking and writing primary data (1167 records, 4 fields): 16 millis CompletedMACS2peakCalling