Job ID = 6529254 SRX = SRX1115695 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: 00:06:15 27945773 reads; of these: 27945773 (100.00%) were unpaired; of these: 1133613 (4.06%) aligned 0 times 20575839 (73.63%) aligned exactly 1 time 6236321 (22.32%) aligned >1 times 95.94% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 3648594 / 26812160 = 0.1361 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 01:45:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.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 01:45:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:07: 1000000 INFO @ Tue, 30 Jun 2020 01:45:13: 2000000 INFO @ Tue, 30 Jun 2020 01:45:19: 3000000 INFO @ Tue, 30 Jun 2020 01:45:25: 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 01:45:31: 5000000 INFO @ Tue, 30 Jun 2020 01:45:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.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 01:45:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:37: 6000000 INFO @ Tue, 30 Jun 2020 01:45:39: 1000000 INFO @ Tue, 30 Jun 2020 01:45:44: 7000000 INFO @ Tue, 30 Jun 2020 01:45:46: 2000000 INFO @ Tue, 30 Jun 2020 01:45:51: 8000000 INFO @ Tue, 30 Jun 2020 01:45:54: 3000000 INFO @ Tue, 30 Jun 2020 01:45:57: 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 01:46:01: 4000000 INFO @ Tue, 30 Jun 2020 01:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.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 01:46:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:04: 10000000 INFO @ Tue, 30 Jun 2020 01:46:08: 1000000 INFO @ Tue, 30 Jun 2020 01:46:08: 5000000 INFO @ Tue, 30 Jun 2020 01:46:11: 11000000 INFO @ Tue, 30 Jun 2020 01:46:15: 2000000 INFO @ Tue, 30 Jun 2020 01:46:16: 6000000 INFO @ Tue, 30 Jun 2020 01:46:18: 12000000 INFO @ Tue, 30 Jun 2020 01:46:22: 3000000 INFO @ Tue, 30 Jun 2020 01:46:23: 7000000 INFO @ Tue, 30 Jun 2020 01:46:25: 13000000 INFO @ Tue, 30 Jun 2020 01:46:30: 4000000 INFO @ Tue, 30 Jun 2020 01:46:30: 8000000 INFO @ Tue, 30 Jun 2020 01:46:32: 14000000 INFO @ Tue, 30 Jun 2020 01:46:37: 5000000 INFO @ Tue, 30 Jun 2020 01:46:38: 9000000 INFO @ Tue, 30 Jun 2020 01:46:39: 15000000 INFO @ Tue, 30 Jun 2020 01:46:44: 6000000 INFO @ Tue, 30 Jun 2020 01:46:45: 10000000 INFO @ Tue, 30 Jun 2020 01:46:46: 16000000 INFO @ Tue, 30 Jun 2020 01:46:51: 7000000 INFO @ Tue, 30 Jun 2020 01:46:53: 11000000 INFO @ Tue, 30 Jun 2020 01:46:54: 17000000 INFO @ Tue, 30 Jun 2020 01:46:58: 8000000 INFO @ Tue, 30 Jun 2020 01:47:00: 12000000 INFO @ Tue, 30 Jun 2020 01:47:01: 18000000 INFO @ Tue, 30 Jun 2020 01:47:05: 9000000 INFO @ Tue, 30 Jun 2020 01:47:08: 13000000 INFO @ Tue, 30 Jun 2020 01:47:08: 19000000 INFO @ Tue, 30 Jun 2020 01:47:12: 10000000 INFO @ Tue, 30 Jun 2020 01:47:15: 14000000 INFO @ Tue, 30 Jun 2020 01:47:16: 20000000 INFO @ Tue, 30 Jun 2020 01:47:19: 11000000 INFO @ Tue, 30 Jun 2020 01:47:23: 15000000 INFO @ Tue, 30 Jun 2020 01:47:23: 21000000 INFO @ Tue, 30 Jun 2020 01:47:27: 12000000 INFO @ Tue, 30 Jun 2020 01:47:30: 16000000 INFO @ Tue, 30 Jun 2020 01:47:30: 22000000 INFO @ Tue, 30 Jun 2020 01:47:34: 13000000 INFO @ Tue, 30 Jun 2020 01:47:38: 17000000 INFO @ Tue, 30 Jun 2020 01:47:38: 23000000 INFO @ Tue, 30 Jun 2020 01:47:39: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:47:39: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:47:39: #1 total tags in treatment: 23163566 INFO @ Tue, 30 Jun 2020 01:47:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:39: #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 01:47:40: #1 tags after filtering in treatment: 23163566 INFO @ Tue, 30 Jun 2020 01:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:40: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:41: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 01:47:41: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:41: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:41: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:41: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:41: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:41: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 01:47:41: #2 alternative fragment length(s) may be 2,45,587 bps INFO @ Tue, 30 Jun 2020 01:47:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.05_model.r WARNING @ Tue, 30 Jun 2020 01:47:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:47:41: #2 You may need to consider one of the other alternative d(s): 2,45,587 WARNING @ Tue, 30 Jun 2020 01:47:41: #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 01:47:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:41: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:47:45: 18000000 INFO @ Tue, 30 Jun 2020 01:47:48: 15000000 INFO @ Tue, 30 Jun 2020 01:47:53: 19000000 INFO @ Tue, 30 Jun 2020 01:47:55: 16000000 INFO @ Tue, 30 Jun 2020 01:48:01: 20000000 INFO @ Tue, 30 Jun 2020 01:48:02: 17000000 INFO @ Tue, 30 Jun 2020 01:48:09: 21000000 INFO @ Tue, 30 Jun 2020 01:48:10: 18000000 INFO @ Tue, 30 Jun 2020 01:48:17: 22000000 INFO @ Tue, 30 Jun 2020 01:48:17: 19000000 INFO @ Tue, 30 Jun 2020 01:48:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:48:24: 20000000 INFO @ Tue, 30 Jun 2020 01:48:25: 23000000 INFO @ Tue, 30 Jun 2020 01:48:26: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:48:26: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:48:26: #1 total tags in treatment: 23163566 INFO @ Tue, 30 Jun 2020 01:48:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:26: #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 01:48:27: #1 tags after filtering in treatment: 23163566 INFO @ Tue, 30 Jun 2020 01:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:27: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:28: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 01:48:28: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:28: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:28: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:28: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:28: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:28: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 01:48:28: #2 alternative fragment length(s) may be 2,45,587 bps INFO @ Tue, 30 Jun 2020 01:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.10_model.r WARNING @ Tue, 30 Jun 2020 01:48:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:28: #2 You may need to consider one of the other alternative d(s): 2,45,587 WARNING @ Tue, 30 Jun 2020 01:48:28: #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 01:48:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:31: 21000000 INFO @ Tue, 30 Jun 2020 01:48:37: 22000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.05_summits.bed INFO @ Tue, 30 Jun 2020 01:48:42: Done! pass1 - making usageList (567 chroms): 1 millis pass2 - checking and writing primary data (2057 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:48:44: 23000000 INFO @ Tue, 30 Jun 2020 01:48:45: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:48:45: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:48:45: #1 total tags in treatment: 23163566 INFO @ Tue, 30 Jun 2020 01:48:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:45: #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 01:48:46: #1 tags after filtering in treatment: 23163566 INFO @ Tue, 30 Jun 2020 01:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:46: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:47: #2 number of paired peaks: 166 WARNING @ Tue, 30 Jun 2020 01:48:47: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:47: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:47: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:47: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:47: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:47: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 01:48:47: #2 alternative fragment length(s) may be 2,45,587 bps INFO @ Tue, 30 Jun 2020 01:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.20_model.r WARNING @ Tue, 30 Jun 2020 01:48:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:47: #2 You may need to consider one of the other alternative d(s): 2,45,587 WARNING @ Tue, 30 Jun 2020 01:48:47: #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 01:48:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:49:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.10_summits.bed INFO @ Tue, 30 Jun 2020 01:49:27: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (845 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115695/SRX1115695.20_summits.bed INFO @ Tue, 30 Jun 2020 01:49:46: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 5 millis CompletedMACS2peakCalling