Job ID = 6529439 SRX = SRX2734369 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: 00:08:03 35559788 reads; of these: 35559788 (100.00%) were unpaired; of these: 1246842 (3.51%) aligned 0 times 29187486 (82.08%) aligned exactly 1 time 5125460 (14.41%) aligned >1 times 96.49% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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] 5933116 / 34312946 = 0.1729 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 02:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.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 02:05:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:35: 1000000 INFO @ Tue, 30 Jun 2020 02:05:43: 2000000 INFO @ Tue, 30 Jun 2020 02:05:51: 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 02:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.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 02:05:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:59: 4000000 INFO @ Tue, 30 Jun 2020 02:06:04: 1000000 INFO @ Tue, 30 Jun 2020 02:06:07: 5000000 INFO @ Tue, 30 Jun 2020 02:06:10: 2000000 INFO @ Tue, 30 Jun 2020 02:06:14: 6000000 INFO @ Tue, 30 Jun 2020 02:06:15: 3000000 INFO @ Tue, 30 Jun 2020 02:06:21: 4000000 INFO @ Tue, 30 Jun 2020 02:06:22: 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 02:06:27: 5000000 INFO @ Tue, 30 Jun 2020 02:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.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 02:06:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:06:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:06:30: 8000000 INFO @ Tue, 30 Jun 2020 02:06:33: 6000000 INFO @ Tue, 30 Jun 2020 02:06:35: 1000000 INFO @ Tue, 30 Jun 2020 02:06:39: 9000000 INFO @ Tue, 30 Jun 2020 02:06:39: 7000000 INFO @ Tue, 30 Jun 2020 02:06:42: 2000000 INFO @ Tue, 30 Jun 2020 02:06:46: 8000000 INFO @ Tue, 30 Jun 2020 02:06:46: 10000000 INFO @ Tue, 30 Jun 2020 02:06:49: 3000000 INFO @ Tue, 30 Jun 2020 02:06:53: 9000000 INFO @ Tue, 30 Jun 2020 02:06:54: 11000000 INFO @ Tue, 30 Jun 2020 02:06:56: 4000000 INFO @ Tue, 30 Jun 2020 02:06:59: 10000000 INFO @ Tue, 30 Jun 2020 02:07:01: 12000000 INFO @ Tue, 30 Jun 2020 02:07:03: 5000000 INFO @ Tue, 30 Jun 2020 02:07:06: 11000000 INFO @ Tue, 30 Jun 2020 02:07:09: 13000000 INFO @ Tue, 30 Jun 2020 02:07:10: 6000000 INFO @ Tue, 30 Jun 2020 02:07:12: 12000000 INFO @ Tue, 30 Jun 2020 02:07:17: 14000000 INFO @ Tue, 30 Jun 2020 02:07:17: 7000000 INFO @ Tue, 30 Jun 2020 02:07:19: 13000000 INFO @ Tue, 30 Jun 2020 02:07:24: 15000000 INFO @ Tue, 30 Jun 2020 02:07:24: 8000000 INFO @ Tue, 30 Jun 2020 02:07:25: 14000000 INFO @ Tue, 30 Jun 2020 02:07:30: 16000000 INFO @ Tue, 30 Jun 2020 02:07:31: 9000000 INFO @ Tue, 30 Jun 2020 02:07:32: 15000000 INFO @ Tue, 30 Jun 2020 02:07:37: 17000000 INFO @ Tue, 30 Jun 2020 02:07:37: 10000000 INFO @ Tue, 30 Jun 2020 02:07:39: 16000000 INFO @ Tue, 30 Jun 2020 02:07:44: 11000000 INFO @ Tue, 30 Jun 2020 02:07:44: 18000000 INFO @ Tue, 30 Jun 2020 02:07:45: 17000000 INFO @ Tue, 30 Jun 2020 02:07:50: 12000000 INFO @ Tue, 30 Jun 2020 02:07:51: 19000000 INFO @ Tue, 30 Jun 2020 02:07:51: 18000000 INFO @ Tue, 30 Jun 2020 02:07:57: 13000000 INFO @ Tue, 30 Jun 2020 02:07:57: 20000000 INFO @ Tue, 30 Jun 2020 02:07:57: 19000000 INFO @ Tue, 30 Jun 2020 02:08:03: 21000000 INFO @ Tue, 30 Jun 2020 02:08:03: 14000000 INFO @ Tue, 30 Jun 2020 02:08:04: 20000000 INFO @ Tue, 30 Jun 2020 02:08:09: 22000000 INFO @ Tue, 30 Jun 2020 02:08:10: 15000000 INFO @ Tue, 30 Jun 2020 02:08:11: 21000000 INFO @ Tue, 30 Jun 2020 02:08:16: 23000000 INFO @ Tue, 30 Jun 2020 02:08:17: 16000000 INFO @ Tue, 30 Jun 2020 02:08:17: 22000000 INFO @ Tue, 30 Jun 2020 02:08:22: 24000000 INFO @ Tue, 30 Jun 2020 02:08:23: 17000000 INFO @ Tue, 30 Jun 2020 02:08:25: 23000000 INFO @ Tue, 30 Jun 2020 02:08:28: 25000000 INFO @ Tue, 30 Jun 2020 02:08:30: 18000000 INFO @ Tue, 30 Jun 2020 02:08:31: 24000000 INFO @ Tue, 30 Jun 2020 02:08:34: 26000000 INFO @ Tue, 30 Jun 2020 02:08:37: 19000000 INFO @ Tue, 30 Jun 2020 02:08:38: 25000000 INFO @ Tue, 30 Jun 2020 02:08:40: 27000000 INFO @ Tue, 30 Jun 2020 02:08:43: 20000000 INFO @ Tue, 30 Jun 2020 02:08:44: 26000000 INFO @ Tue, 30 Jun 2020 02:08:46: 28000000 INFO @ Tue, 30 Jun 2020 02:08:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:08:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:08:49: #1 total tags in treatment: 28379830 INFO @ Tue, 30 Jun 2020 02:08:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:08:49: #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 02:08:50: #1 tags after filtering in treatment: 28379775 INFO @ Tue, 30 Jun 2020 02:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:08:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:08:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:08:50: 21000000 INFO @ Tue, 30 Jun 2020 02:08:51: 27000000 INFO @ Tue, 30 Jun 2020 02:08:52: #2 number of paired peaks: 143 WARNING @ Tue, 30 Jun 2020 02:08:52: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 30 Jun 2020 02:08:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:08:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:08:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:08:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:08:52: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:08:52: #2 alternative fragment length(s) may be 1,46,48,132,435,552 bps INFO @ Tue, 30 Jun 2020 02:08:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.05_model.r WARNING @ Tue, 30 Jun 2020 02:08:52: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:08:52: #2 You may need to consider one of the other alternative d(s): 1,46,48,132,435,552 WARNING @ Tue, 30 Jun 2020 02:08:52: #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 02:08:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:08:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:08:56: 22000000 INFO @ Tue, 30 Jun 2020 02:08:57: 28000000 INFO @ Tue, 30 Jun 2020 02:09:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:09:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:09:00: #1 total tags in treatment: 28379830 INFO @ Tue, 30 Jun 2020 02:09:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:09:00: #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 02:09:01: #1 tags after filtering in treatment: 28379775 INFO @ Tue, 30 Jun 2020 02:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:09:01: #1 finished! INFO @ Tue, 30 Jun 2020 02:09:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:09:02: #2 number of paired peaks: 143 WARNING @ Tue, 30 Jun 2020 02:09:02: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 30 Jun 2020 02:09:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:09:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:09:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:09:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:09:02: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:09:02: #2 alternative fragment length(s) may be 1,46,48,132,435,552 bps INFO @ Tue, 30 Jun 2020 02:09:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.10_model.r WARNING @ Tue, 30 Jun 2020 02:09:02: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:09:02: #2 You may need to consider one of the other alternative d(s): 1,46,48,132,435,552 WARNING @ Tue, 30 Jun 2020 02:09:02: #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 02:09:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:09:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:09:03: 23000000 INFO @ Tue, 30 Jun 2020 02:09:09: 24000000 INFO @ Tue, 30 Jun 2020 02:09:15: 25000000 INFO @ Tue, 30 Jun 2020 02:09:20: 26000000 INFO @ Tue, 30 Jun 2020 02:09:26: 27000000 INFO @ Tue, 30 Jun 2020 02:09:32: 28000000 INFO @ Tue, 30 Jun 2020 02:09:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:09:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:09:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:09:34: #1 total tags in treatment: 28379830 INFO @ Tue, 30 Jun 2020 02:09:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:09:34: #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 02:09:36: #1 tags after filtering in treatment: 28379775 INFO @ Tue, 30 Jun 2020 02:09:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:09:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:09:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:09:37: #2 number of paired peaks: 143 WARNING @ Tue, 30 Jun 2020 02:09:37: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 30 Jun 2020 02:09:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:09:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:09:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:09:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:09:37: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:09:37: #2 alternative fragment length(s) may be 1,46,48,132,435,552 bps INFO @ Tue, 30 Jun 2020 02:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.20_model.r WARNING @ Tue, 30 Jun 2020 02:09:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:09:37: #2 You may need to consider one of the other alternative d(s): 1,46,48,132,435,552 WARNING @ Tue, 30 Jun 2020 02:09:37: #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 02:09:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:09:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.05_summits.bed INFO @ Tue, 30 Jun 2020 02:09:55: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (876 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.10_summits.bed INFO @ Tue, 30 Jun 2020 02:10:08: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:10:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2734369/SRX2734369.20_summits.bed INFO @ Tue, 30 Jun 2020 02:10:44: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 5 millis CompletedMACS2peakCalling