Job ID = 6529499 SRX = SRX287845 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: 00:04:51 17761171 reads; of these: 17761171 (100.00%) were unpaired; of these: 1061829 (5.98%) aligned 0 times 12962629 (72.98%) aligned exactly 1 time 3736713 (21.04%) aligned >1 times 94.02% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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 8 files... [bam_rmdupse_core] 1639480 / 16699342 = 0.0982 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 02:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.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 02:27:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:27:36: 1000000 INFO @ Tue, 30 Jun 2020 02:27:41: 2000000 INFO @ Tue, 30 Jun 2020 02:27:47: 3000000 INFO @ Tue, 30 Jun 2020 02:27:52: 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 02:27:58: 5000000 INFO @ Tue, 30 Jun 2020 02:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.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 02:27:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:28:04: 6000000 INFO @ Tue, 30 Jun 2020 02:28:05: 1000000 INFO @ Tue, 30 Jun 2020 02:28:09: 7000000 INFO @ Tue, 30 Jun 2020 02:28:11: 2000000 INFO @ Tue, 30 Jun 2020 02:28:15: 8000000 INFO @ Tue, 30 Jun 2020 02:28:16: 3000000 INFO @ Tue, 30 Jun 2020 02:28:21: 9000000 INFO @ Tue, 30 Jun 2020 02:28:22: 4000000 INFO @ Tue, 30 Jun 2020 02:28:27: 10000000 INFO @ Tue, 30 Jun 2020 02:28:27: 5000000 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 02:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.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 02:28:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:28:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:28:32: 11000000 INFO @ Tue, 30 Jun 2020 02:28:33: 6000000 INFO @ Tue, 30 Jun 2020 02:28:35: 1000000 INFO @ Tue, 30 Jun 2020 02:28:38: 12000000 INFO @ Tue, 30 Jun 2020 02:28:39: 7000000 INFO @ Tue, 30 Jun 2020 02:28:41: 2000000 INFO @ Tue, 30 Jun 2020 02:28:44: 8000000 INFO @ Tue, 30 Jun 2020 02:28:45: 13000000 INFO @ Tue, 30 Jun 2020 02:28:47: 3000000 INFO @ Tue, 30 Jun 2020 02:28:50: 9000000 INFO @ Tue, 30 Jun 2020 02:28:51: 14000000 INFO @ Tue, 30 Jun 2020 02:28:52: 4000000 INFO @ Tue, 30 Jun 2020 02:28:55: 10000000 INFO @ Tue, 30 Jun 2020 02:28:57: 15000000 INFO @ Tue, 30 Jun 2020 02:28:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:28:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:28:57: #1 total tags in treatment: 15059862 INFO @ Tue, 30 Jun 2020 02:28:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:57: #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 02:28:58: #1 tags after filtering in treatment: 15059861 INFO @ Tue, 30 Jun 2020 02:28:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:58: 5000000 INFO @ Tue, 30 Jun 2020 02:28:59: #2 number of paired peaks: 309 WARNING @ Tue, 30 Jun 2020 02:28:59: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:59: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:28:59: #2 alternative fragment length(s) may be 3,44,549 bps INFO @ Tue, 30 Jun 2020 02:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.05_model.r WARNING @ Tue, 30 Jun 2020 02:28:59: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:28:59: #2 You may need to consider one of the other alternative d(s): 3,44,549 WARNING @ Tue, 30 Jun 2020 02:28:59: #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 02:28:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:01: 11000000 INFO @ Tue, 30 Jun 2020 02:29:03: 6000000 INFO @ Tue, 30 Jun 2020 02:29:06: 12000000 INFO @ Tue, 30 Jun 2020 02:29:09: 7000000 INFO @ Tue, 30 Jun 2020 02:29:12: 13000000 INFO @ Tue, 30 Jun 2020 02:29:15: 8000000 INFO @ Tue, 30 Jun 2020 02:29:18: 14000000 INFO @ Tue, 30 Jun 2020 02:29:20: 9000000 INFO @ Tue, 30 Jun 2020 02:29:24: 15000000 INFO @ Tue, 30 Jun 2020 02:29:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:29:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:29:24: #1 total tags in treatment: 15059862 INFO @ Tue, 30 Jun 2020 02:29:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:24: #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 02:29:25: #1 tags after filtering in treatment: 15059861 INFO @ Tue, 30 Jun 2020 02:29:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:29:25: 10000000 INFO @ Tue, 30 Jun 2020 02:29:26: #2 number of paired peaks: 309 WARNING @ Tue, 30 Jun 2020 02:29:26: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:26: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:29:26: #2 alternative fragment length(s) may be 3,44,549 bps INFO @ Tue, 30 Jun 2020 02:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.10_model.r WARNING @ Tue, 30 Jun 2020 02:29:26: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:29:26: #2 You may need to consider one of the other alternative d(s): 3,44,549 WARNING @ Tue, 30 Jun 2020 02:29:26: #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 02:29:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:31: 11000000 INFO @ Tue, 30 Jun 2020 02:29:36: 12000000 INFO @ Tue, 30 Jun 2020 02:29:42: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:29:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.05_summits.bed INFO @ Tue, 30 Jun 2020 02:29:45: Done! pass1 - making usageList (520 chroms): 1 millis pass2 - checking and writing primary data (2047 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:29:47: 14000000 INFO @ Tue, 30 Jun 2020 02:29:53: 15000000 INFO @ Tue, 30 Jun 2020 02:29:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:29:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:29:53: #1 total tags in treatment: 15059862 INFO @ Tue, 30 Jun 2020 02:29:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:53: #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 02:29:54: #1 tags after filtering in treatment: 15059861 INFO @ Tue, 30 Jun 2020 02:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:29:55: #2 number of paired peaks: 309 WARNING @ Tue, 30 Jun 2020 02:29:55: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:55: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:29:55: #2 alternative fragment length(s) may be 3,44,549 bps INFO @ Tue, 30 Jun 2020 02:29:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.20_model.r WARNING @ Tue, 30 Jun 2020 02:29:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:29:55: #2 You may need to consider one of the other alternative d(s): 3,44,549 WARNING @ Tue, 30 Jun 2020 02:29:55: #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 02:29:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:30:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:30:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:30:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.10_summits.bed INFO @ Tue, 30 Jun 2020 02:30:11: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (1638 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:30:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287845/SRX287845.20_summits.bed INFO @ Tue, 30 Jun 2020 02:30:39: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 9 millis CompletedMACS2peakCalling