Job ID = 6529412 SRX = SRX2564148 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: 00:12:32 39720181 reads; of these: 39720181 (100.00%) were unpaired; of these: 16686641 (42.01%) aligned 0 times 16881290 (42.50%) aligned exactly 1 time 6152250 (15.49%) aligned >1 times 57.99% overall alignment rate Time searching: 00:12:32 Overall time: 00:12:32 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] 4611967 / 23033540 = 0.2002 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 02:16:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.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 02:16:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:58: 1000000 INFO @ Tue, 30 Jun 2020 02:17:06: 2000000 INFO @ Tue, 30 Jun 2020 02:17:15: 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 02:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.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 02:17:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:23: 4000000 INFO @ Tue, 30 Jun 2020 02:17:29: 1000000 INFO @ Tue, 30 Jun 2020 02:17:32: 5000000 INFO @ Tue, 30 Jun 2020 02:17:38: 2000000 INFO @ Tue, 30 Jun 2020 02:17:41: 6000000 INFO @ Tue, 30 Jun 2020 02:17:47: 3000000 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 02:17:50: 7000000 INFO @ Tue, 30 Jun 2020 02:17:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.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 02:17:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:56: 4000000 INFO @ Tue, 30 Jun 2020 02:17:58: 8000000 INFO @ Tue, 30 Jun 2020 02:17:59: 1000000 INFO @ Tue, 30 Jun 2020 02:18:06: 5000000 INFO @ Tue, 30 Jun 2020 02:18:07: 9000000 INFO @ Tue, 30 Jun 2020 02:18:08: 2000000 INFO @ Tue, 30 Jun 2020 02:18:15: 6000000 INFO @ Tue, 30 Jun 2020 02:18:16: 10000000 INFO @ Tue, 30 Jun 2020 02:18:17: 3000000 INFO @ Tue, 30 Jun 2020 02:18:24: 7000000 INFO @ Tue, 30 Jun 2020 02:18:25: 11000000 INFO @ Tue, 30 Jun 2020 02:18:26: 4000000 INFO @ Tue, 30 Jun 2020 02:18:32: 8000000 INFO @ Tue, 30 Jun 2020 02:18:34: 12000000 INFO @ Tue, 30 Jun 2020 02:18:35: 5000000 INFO @ Tue, 30 Jun 2020 02:18:41: 9000000 INFO @ Tue, 30 Jun 2020 02:18:43: 13000000 INFO @ Tue, 30 Jun 2020 02:18:44: 6000000 INFO @ Tue, 30 Jun 2020 02:18:50: 10000000 INFO @ Tue, 30 Jun 2020 02:18:51: 14000000 INFO @ Tue, 30 Jun 2020 02:18:52: 7000000 INFO @ Tue, 30 Jun 2020 02:18:59: 11000000 INFO @ Tue, 30 Jun 2020 02:19:01: 15000000 INFO @ Tue, 30 Jun 2020 02:19:01: 8000000 INFO @ Tue, 30 Jun 2020 02:19:08: 12000000 INFO @ Tue, 30 Jun 2020 02:19:10: 16000000 INFO @ Tue, 30 Jun 2020 02:19:10: 9000000 INFO @ Tue, 30 Jun 2020 02:19:16: 13000000 INFO @ Tue, 30 Jun 2020 02:19:18: 17000000 INFO @ Tue, 30 Jun 2020 02:19:19: 10000000 INFO @ Tue, 30 Jun 2020 02:19:25: 14000000 INFO @ Tue, 30 Jun 2020 02:19:27: 18000000 INFO @ Tue, 30 Jun 2020 02:19:27: 11000000 INFO @ Tue, 30 Jun 2020 02:19:31: #1 tag size is determined as 70 bps INFO @ Tue, 30 Jun 2020 02:19:31: #1 tag size = 70 INFO @ Tue, 30 Jun 2020 02:19:31: #1 total tags in treatment: 18421573 INFO @ Tue, 30 Jun 2020 02:19:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:31: #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 02:19:31: #1 tags after filtering in treatment: 18421573 INFO @ Tue, 30 Jun 2020 02:19:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:33: #2 number of paired peaks: 563 WARNING @ Tue, 30 Jun 2020 02:19:33: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:33: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:19:33: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 30 Jun 2020 02:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.05_model.r WARNING @ Tue, 30 Jun 2020 02:19:33: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:33: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 30 Jun 2020 02:19:33: #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 02:19:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:34: 15000000 INFO @ Tue, 30 Jun 2020 02:19:36: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:19:43: 16000000 INFO @ Tue, 30 Jun 2020 02:19:44: 13000000 INFO @ Tue, 30 Jun 2020 02:19:51: 17000000 INFO @ Tue, 30 Jun 2020 02:19:53: 14000000 INFO @ Tue, 30 Jun 2020 02:20:00: 18000000 INFO @ Tue, 30 Jun 2020 02:20:02: 15000000 INFO @ Tue, 30 Jun 2020 02:20:04: #1 tag size is determined as 70 bps INFO @ Tue, 30 Jun 2020 02:20:04: #1 tag size = 70 INFO @ Tue, 30 Jun 2020 02:20:04: #1 total tags in treatment: 18421573 INFO @ Tue, 30 Jun 2020 02:20:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:04: #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 02:20:04: #1 tags after filtering in treatment: 18421573 INFO @ Tue, 30 Jun 2020 02:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:06: #2 number of paired peaks: 563 WARNING @ Tue, 30 Jun 2020 02:20:06: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:06: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:06: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:06: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:06: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:06: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:20:06: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 30 Jun 2020 02:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.10_model.r WARNING @ Tue, 30 Jun 2020 02:20:06: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:06: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 30 Jun 2020 02:20:06: #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 02:20:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:10: 16000000 INFO @ Tue, 30 Jun 2020 02:20:18: 17000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.05_summits.bed INFO @ Tue, 30 Jun 2020 02:20:22: Done! pass1 - making usageList (678 chroms): 2 millis pass2 - checking and writing primary data (2217 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:20:26: 18000000 INFO @ Tue, 30 Jun 2020 02:20:29: #1 tag size is determined as 70 bps INFO @ Tue, 30 Jun 2020 02:20:29: #1 tag size = 70 INFO @ Tue, 30 Jun 2020 02:20:29: #1 total tags in treatment: 18421573 INFO @ Tue, 30 Jun 2020 02:20:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:29: #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 02:20:30: #1 tags after filtering in treatment: 18421573 INFO @ Tue, 30 Jun 2020 02:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:30: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:31: #2 number of paired peaks: 563 WARNING @ Tue, 30 Jun 2020 02:20:31: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:31: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:20:31: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 30 Jun 2020 02:20:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.20_model.r WARNING @ Tue, 30 Jun 2020 02:20:31: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:31: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 30 Jun 2020 02:20:31: #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 02:20:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.10_summits.bed INFO @ Tue, 30 Jun 2020 02:20:55: Done! pass1 - making usageList (545 chroms): 1 millis pass2 - checking and writing primary data (1647 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564148/SRX2564148.20_summits.bed INFO @ Tue, 30 Jun 2020 02:21:20: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1295 records, 4 fields): 15 millis CompletedMACS2peakCalling