Job ID = 6529244 SRX = SRX1085382 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: 00:07:40 33736384 reads; of these: 33736384 (100.00%) were unpaired; of these: 1378560 (4.09%) aligned 0 times 25106622 (74.42%) aligned exactly 1 time 7251202 (21.49%) aligned >1 times 95.91% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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] 3686097 / 32357824 = 0.1139 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 01:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.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 01:41:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:41:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:41:56: 1000000 INFO @ Tue, 30 Jun 2020 01:42:04: 2000000 INFO @ Tue, 30 Jun 2020 01:42:12: 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 01:42:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.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 01:42:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:42:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:42:21: 4000000 INFO @ Tue, 30 Jun 2020 01:42:26: 1000000 INFO @ Tue, 30 Jun 2020 01:42:29: 5000000 INFO @ Tue, 30 Jun 2020 01:42:35: 2000000 INFO @ Tue, 30 Jun 2020 01:42:38: 6000000 INFO @ Tue, 30 Jun 2020 01:42:43: 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 01:42:47: 7000000 INFO @ Tue, 30 Jun 2020 01:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.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 01:42:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:42:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:42:52: 4000000 INFO @ Tue, 30 Jun 2020 01:42:55: 1000000 INFO @ Tue, 30 Jun 2020 01:42:55: 8000000 INFO @ Tue, 30 Jun 2020 01:43:00: 5000000 INFO @ Tue, 30 Jun 2020 01:43:02: 2000000 INFO @ Tue, 30 Jun 2020 01:43:04: 9000000 INFO @ Tue, 30 Jun 2020 01:43:09: 6000000 INFO @ Tue, 30 Jun 2020 01:43:09: 3000000 INFO @ Tue, 30 Jun 2020 01:43:12: 10000000 INFO @ Tue, 30 Jun 2020 01:43:16: 4000000 INFO @ Tue, 30 Jun 2020 01:43:17: 7000000 INFO @ Tue, 30 Jun 2020 01:43:20: 11000000 INFO @ Tue, 30 Jun 2020 01:43:24: 5000000 INFO @ Tue, 30 Jun 2020 01:43:26: 8000000 INFO @ Tue, 30 Jun 2020 01:43:29: 12000000 INFO @ Tue, 30 Jun 2020 01:43:31: 6000000 INFO @ Tue, 30 Jun 2020 01:43:34: 9000000 INFO @ Tue, 30 Jun 2020 01:43:37: 13000000 INFO @ Tue, 30 Jun 2020 01:43:38: 7000000 INFO @ Tue, 30 Jun 2020 01:43:42: 10000000 INFO @ Tue, 30 Jun 2020 01:43:45: 14000000 INFO @ Tue, 30 Jun 2020 01:43:45: 8000000 INFO @ Tue, 30 Jun 2020 01:43:50: 11000000 INFO @ Tue, 30 Jun 2020 01:43:53: 9000000 INFO @ Tue, 30 Jun 2020 01:43:53: 15000000 INFO @ Tue, 30 Jun 2020 01:43:58: 12000000 INFO @ Tue, 30 Jun 2020 01:44:00: 10000000 INFO @ Tue, 30 Jun 2020 01:44:01: 16000000 INFO @ Tue, 30 Jun 2020 01:44:06: 13000000 INFO @ Tue, 30 Jun 2020 01:44:07: 11000000 INFO @ Tue, 30 Jun 2020 01:44:09: 17000000 INFO @ Tue, 30 Jun 2020 01:44:13: 14000000 INFO @ Tue, 30 Jun 2020 01:44:14: 12000000 INFO @ Tue, 30 Jun 2020 01:44:16: 18000000 INFO @ Tue, 30 Jun 2020 01:44:21: 13000000 INFO @ Tue, 30 Jun 2020 01:44:21: 15000000 INFO @ Tue, 30 Jun 2020 01:44:24: 19000000 INFO @ Tue, 30 Jun 2020 01:44:27: 14000000 INFO @ Tue, 30 Jun 2020 01:44:29: 16000000 INFO @ Tue, 30 Jun 2020 01:44:31: 20000000 INFO @ Tue, 30 Jun 2020 01:44:34: 15000000 INFO @ Tue, 30 Jun 2020 01:44:36: 17000000 INFO @ Tue, 30 Jun 2020 01:44:39: 21000000 INFO @ Tue, 30 Jun 2020 01:44:41: 16000000 INFO @ Tue, 30 Jun 2020 01:44:44: 18000000 INFO @ Tue, 30 Jun 2020 01:44:46: 22000000 INFO @ Tue, 30 Jun 2020 01:44:47: 17000000 INFO @ Tue, 30 Jun 2020 01:44:51: 19000000 INFO @ Tue, 30 Jun 2020 01:44:54: 23000000 INFO @ Tue, 30 Jun 2020 01:44:54: 18000000 INFO @ Tue, 30 Jun 2020 01:44:59: 20000000 INFO @ Tue, 30 Jun 2020 01:45:01: 19000000 INFO @ Tue, 30 Jun 2020 01:45:02: 24000000 INFO @ Tue, 30 Jun 2020 01:45:06: 21000000 INFO @ Tue, 30 Jun 2020 01:45:07: 20000000 INFO @ Tue, 30 Jun 2020 01:45:10: 25000000 INFO @ Tue, 30 Jun 2020 01:45:13: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:45:14: 21000000 INFO @ Tue, 30 Jun 2020 01:45:17: 26000000 INFO @ Tue, 30 Jun 2020 01:45:21: 23000000 INFO @ Tue, 30 Jun 2020 01:45:21: 22000000 INFO @ Tue, 30 Jun 2020 01:45:24: 27000000 INFO @ Tue, 30 Jun 2020 01:45:27: 23000000 INFO @ Tue, 30 Jun 2020 01:45:29: 24000000 INFO @ Tue, 30 Jun 2020 01:45:32: 28000000 INFO @ Tue, 30 Jun 2020 01:45:35: 24000000 INFO @ Tue, 30 Jun 2020 01:45:36: 25000000 INFO @ Tue, 30 Jun 2020 01:45:37: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:45:37: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:45:37: #1 total tags in treatment: 28671727 INFO @ Tue, 30 Jun 2020 01:45:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:45:37: #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 01:45:38: #1 tags after filtering in treatment: 28671727 INFO @ Tue, 30 Jun 2020 01:45:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:45:38: #1 finished! INFO @ Tue, 30 Jun 2020 01:45:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:45:40: #2 number of paired peaks: 169 WARNING @ Tue, 30 Jun 2020 01:45:40: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 30 Jun 2020 01:45:40: start model_add_line... INFO @ Tue, 30 Jun 2020 01:45:40: start X-correlation... INFO @ Tue, 30 Jun 2020 01:45:40: end of X-cor INFO @ Tue, 30 Jun 2020 01:45:40: #2 finished! INFO @ Tue, 30 Jun 2020 01:45:40: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 01:45:40: #2 alternative fragment length(s) may be 1,35,574,592 bps INFO @ Tue, 30 Jun 2020 01:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.05_model.r WARNING @ Tue, 30 Jun 2020 01:45:40: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:45:40: #2 You may need to consider one of the other alternative d(s): 1,35,574,592 WARNING @ Tue, 30 Jun 2020 01:45:40: #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 01:45:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:45:41: 25000000 INFO @ Tue, 30 Jun 2020 01:45:43: 26000000 INFO @ Tue, 30 Jun 2020 01:45:48: 26000000 INFO @ Tue, 30 Jun 2020 01:45:50: 27000000 INFO @ Tue, 30 Jun 2020 01:45:55: 27000000 INFO @ Tue, 30 Jun 2020 01:45:57: 28000000 INFO @ Tue, 30 Jun 2020 01:46:01: 28000000 INFO @ Tue, 30 Jun 2020 01:46:02: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:46:02: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:46:02: #1 total tags in treatment: 28671727 INFO @ Tue, 30 Jun 2020 01:46:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:02: #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 01:46:03: #1 tags after filtering in treatment: 28671727 INFO @ Tue, 30 Jun 2020 01:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:05: #2 number of paired peaks: 169 WARNING @ Tue, 30 Jun 2020 01:46:05: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:05: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:05: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:05: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:05: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:05: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 01:46:05: #2 alternative fragment length(s) may be 1,35,574,592 bps INFO @ Tue, 30 Jun 2020 01:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.10_model.r WARNING @ Tue, 30 Jun 2020 01:46:05: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:46:05: #2 You may need to consider one of the other alternative d(s): 1,35,574,592 WARNING @ Tue, 30 Jun 2020 01:46:05: #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 01:46:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:06: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:46:06: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:46:06: #1 total tags in treatment: 28671727 INFO @ Tue, 30 Jun 2020 01:46:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:06: #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 01:46:07: #1 tags after filtering in treatment: 28671727 INFO @ Tue, 30 Jun 2020 01:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:07: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:09: #2 number of paired peaks: 169 WARNING @ Tue, 30 Jun 2020 01:46:09: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:09: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:09: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:09: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:09: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:09: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 01:46:09: #2 alternative fragment length(s) may be 1,35,574,592 bps INFO @ Tue, 30 Jun 2020 01:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.20_model.r WARNING @ Tue, 30 Jun 2020 01:46:09: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:46:09: #2 You may need to consider one of the other alternative d(s): 1,35,574,592 WARNING @ Tue, 30 Jun 2020 01:46:09: #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 01:46:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.05_summits.bed INFO @ Tue, 30 Jun 2020 01:46:46: Done! pass1 - making usageList (573 chroms): 2 millis pass2 - checking and writing primary data (2808 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:46:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.10_summits.bed INFO @ Tue, 30 Jun 2020 01:47:11: Done! pass1 - making usageList (389 chroms): 1 millis pass2 - checking and writing primary data (1083 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1085382/SRX1085382.20_summits.bed INFO @ Tue, 30 Jun 2020 01:47:15: Done! pass1 - making usageList (130 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 9 millis CompletedMACS2peakCalling