Job ID = 6529345 SRX = SRX193328 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: 00:12:12 35151074 reads; of these: 35151074 (100.00%) were unpaired; of these: 1818408 (5.17%) aligned 0 times 22215651 (63.20%) aligned exactly 1 time 11117015 (31.63%) aligned >1 times 94.83% overall alignment rate Time searching: 00:12:12 Overall time: 00:12:12 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] 7186315 / 33332666 = 0.2156 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 02:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.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 02:16:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:32: 1000000 INFO @ Tue, 30 Jun 2020 02:16:39: 2000000 INFO @ Tue, 30 Jun 2020 02:16:47: 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 02:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.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 02:16:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:55: 4000000 INFO @ Tue, 30 Jun 2020 02:17:02: 1000000 INFO @ Tue, 30 Jun 2020 02:17:03: 5000000 INFO @ Tue, 30 Jun 2020 02:17:11: 2000000 INFO @ Tue, 30 Jun 2020 02:17:12: 6000000 INFO @ Tue, 30 Jun 2020 02:17:19: 3000000 INFO @ Tue, 30 Jun 2020 02:17:20: 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 02:17:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.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 02:17:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:27: 4000000 INFO @ Tue, 30 Jun 2020 02:17:29: 8000000 INFO @ Tue, 30 Jun 2020 02:17:33: 1000000 INFO @ Tue, 30 Jun 2020 02:17:35: 5000000 INFO @ Tue, 30 Jun 2020 02:17:38: 9000000 INFO @ Tue, 30 Jun 2020 02:17:43: 2000000 INFO @ Tue, 30 Jun 2020 02:17:43: 6000000 INFO @ Tue, 30 Jun 2020 02:17:47: 10000000 INFO @ Tue, 30 Jun 2020 02:17:52: 7000000 INFO @ Tue, 30 Jun 2020 02:17:52: 3000000 INFO @ Tue, 30 Jun 2020 02:17:56: 11000000 INFO @ Tue, 30 Jun 2020 02:18:00: 8000000 INFO @ Tue, 30 Jun 2020 02:18:01: 4000000 INFO @ Tue, 30 Jun 2020 02:18:05: 12000000 INFO @ Tue, 30 Jun 2020 02:18:08: 9000000 INFO @ Tue, 30 Jun 2020 02:18:10: 5000000 INFO @ Tue, 30 Jun 2020 02:18:14: 13000000 INFO @ Tue, 30 Jun 2020 02:18:17: 10000000 INFO @ Tue, 30 Jun 2020 02:18:18: 6000000 INFO @ Tue, 30 Jun 2020 02:18:23: 14000000 INFO @ Tue, 30 Jun 2020 02:18:25: 11000000 INFO @ Tue, 30 Jun 2020 02:18:27: 7000000 INFO @ Tue, 30 Jun 2020 02:18:32: 15000000 INFO @ Tue, 30 Jun 2020 02:18:34: 12000000 INFO @ Tue, 30 Jun 2020 02:18:36: 8000000 INFO @ Tue, 30 Jun 2020 02:18:41: 16000000 INFO @ Tue, 30 Jun 2020 02:18:42: 13000000 INFO @ Tue, 30 Jun 2020 02:18:45: 9000000 INFO @ Tue, 30 Jun 2020 02:18:50: 17000000 INFO @ Tue, 30 Jun 2020 02:18:51: 14000000 INFO @ Tue, 30 Jun 2020 02:18:55: 10000000 INFO @ Tue, 30 Jun 2020 02:19:00: 15000000 INFO @ Tue, 30 Jun 2020 02:19:00: 18000000 INFO @ Tue, 30 Jun 2020 02:19:04: 11000000 INFO @ Tue, 30 Jun 2020 02:19:09: 16000000 INFO @ Tue, 30 Jun 2020 02:19:09: 19000000 INFO @ Tue, 30 Jun 2020 02:19:13: 12000000 INFO @ Tue, 30 Jun 2020 02:19:17: 17000000 INFO @ Tue, 30 Jun 2020 02:19:18: 20000000 INFO @ Tue, 30 Jun 2020 02:19:22: 13000000 INFO @ Tue, 30 Jun 2020 02:19:26: 18000000 INFO @ Tue, 30 Jun 2020 02:19:27: 21000000 INFO @ Tue, 30 Jun 2020 02:19:31: 14000000 INFO @ Tue, 30 Jun 2020 02:19:35: 19000000 INFO @ Tue, 30 Jun 2020 02:19:37: 22000000 INFO @ Tue, 30 Jun 2020 02:19:41: 15000000 INFO @ Tue, 30 Jun 2020 02:19:44: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:19:47: 23000000 INFO @ Tue, 30 Jun 2020 02:19:50: 16000000 INFO @ Tue, 30 Jun 2020 02:19:53: 21000000 INFO @ Tue, 30 Jun 2020 02:19:56: 24000000 INFO @ Tue, 30 Jun 2020 02:19:59: 17000000 INFO @ Tue, 30 Jun 2020 02:20:03: 22000000 INFO @ Tue, 30 Jun 2020 02:20:06: 25000000 INFO @ Tue, 30 Jun 2020 02:20:09: 18000000 INFO @ Tue, 30 Jun 2020 02:20:12: 23000000 INFO @ Tue, 30 Jun 2020 02:20:15: 26000000 INFO @ Tue, 30 Jun 2020 02:20:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:20:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:20:17: #1 total tags in treatment: 26146351 INFO @ Tue, 30 Jun 2020 02:20:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:17: #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 02:20:18: #1 tags after filtering in treatment: 26146294 INFO @ Tue, 30 Jun 2020 02:20:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:19: 19000000 INFO @ Tue, 30 Jun 2020 02:20:20: #2 number of paired peaks: 784 WARNING @ Tue, 30 Jun 2020 02:20:20: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:20: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:20:20: #2 alternative fragment length(s) may be 1,41,598 bps INFO @ Tue, 30 Jun 2020 02:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.05_model.r WARNING @ Tue, 30 Jun 2020 02:20:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:20: #2 You may need to consider one of the other alternative d(s): 1,41,598 WARNING @ Tue, 30 Jun 2020 02:20:20: #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 02:20:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:20: 24000000 INFO @ Tue, 30 Jun 2020 02:20:28: 20000000 INFO @ Tue, 30 Jun 2020 02:20:29: 25000000 INFO @ Tue, 30 Jun 2020 02:20:37: 21000000 INFO @ Tue, 30 Jun 2020 02:20:38: 26000000 INFO @ Tue, 30 Jun 2020 02:20:39: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:20:39: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:20:39: #1 total tags in treatment: 26146351 INFO @ Tue, 30 Jun 2020 02:20:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:39: #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 02:20:40: #1 tags after filtering in treatment: 26146294 INFO @ Tue, 30 Jun 2020 02:20:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:42: #2 number of paired peaks: 784 WARNING @ Tue, 30 Jun 2020 02:20:42: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:42: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:42: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:42: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:42: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:42: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:20:42: #2 alternative fragment length(s) may be 1,41,598 bps INFO @ Tue, 30 Jun 2020 02:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.10_model.r WARNING @ Tue, 30 Jun 2020 02:20:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:42: #2 You may need to consider one of the other alternative d(s): 1,41,598 WARNING @ Tue, 30 Jun 2020 02:20:42: #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 02:20:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:47: 22000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:20:55: 23000000 INFO @ Tue, 30 Jun 2020 02:21:03: 24000000 INFO @ Tue, 30 Jun 2020 02:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:12: 25000000 INFO @ Tue, 30 Jun 2020 02:21:20: 26000000 INFO @ Tue, 30 Jun 2020 02:21:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:21:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:21:22: #1 total tags in treatment: 26146351 INFO @ Tue, 30 Jun 2020 02:21:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:22: #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 02:21:22: #1 tags after filtering in treatment: 26146294 INFO @ Tue, 30 Jun 2020 02:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:24: #2 number of paired peaks: 784 WARNING @ Tue, 30 Jun 2020 02:21:24: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:24: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:21:24: #2 alternative fragment length(s) may be 1,41,598 bps INFO @ Tue, 30 Jun 2020 02:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.20_model.r WARNING @ Tue, 30 Jun 2020 02:21:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:24: #2 You may need to consider one of the other alternative d(s): 1,41,598 WARNING @ Tue, 30 Jun 2020 02:21:24: #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 02:21:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.05_summits.bed INFO @ Tue, 30 Jun 2020 02:21:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.10_summits.bed INFO @ Tue, 30 Jun 2020 02:21:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:22:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193328/SRX193328.20_summits.bed INFO @ Tue, 30 Jun 2020 02:22:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling