Job ID = 6530073 SRX = SRX750084 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: 00:32:39 84929115 reads; of these: 84929115 (100.00%) were unpaired; of these: 2896187 (3.41%) aligned 0 times 57771033 (68.02%) aligned exactly 1 time 24261895 (28.57%) aligned >1 times 96.59% overall alignment rate Time searching: 00:32:39 Overall time: 00:32:39 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 36 files... [bam_rmdupse_core] 53351902 / 82032928 = 0.6504 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 03:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.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 03:55:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:55:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:56:06: 1000000 INFO @ Tue, 30 Jun 2020 03:56:13: 2000000 INFO @ Tue, 30 Jun 2020 03:56:20: 3000000 INFO @ Tue, 30 Jun 2020 03:56:27: 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 03:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.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 03:56:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:56:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:56:34: 5000000 INFO @ Tue, 30 Jun 2020 03:56:37: 1000000 INFO @ Tue, 30 Jun 2020 03:56:42: 6000000 INFO @ Tue, 30 Jun 2020 03:56:44: 2000000 INFO @ Tue, 30 Jun 2020 03:56:49: 7000000 INFO @ Tue, 30 Jun 2020 03:56:52: 3000000 INFO @ Tue, 30 Jun 2020 03:56:57: 8000000 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 03:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.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 03:56:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:56:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:57:00: 4000000 INFO @ Tue, 30 Jun 2020 03:57:05: 9000000 INFO @ Tue, 30 Jun 2020 03:57:07: 1000000 INFO @ Tue, 30 Jun 2020 03:57:07: 5000000 INFO @ Tue, 30 Jun 2020 03:57:12: 10000000 INFO @ Tue, 30 Jun 2020 03:57:15: 2000000 INFO @ Tue, 30 Jun 2020 03:57:15: 6000000 INFO @ Tue, 30 Jun 2020 03:57:20: 11000000 INFO @ Tue, 30 Jun 2020 03:57:23: 7000000 INFO @ Tue, 30 Jun 2020 03:57:23: 3000000 INFO @ Tue, 30 Jun 2020 03:57:28: 12000000 INFO @ Tue, 30 Jun 2020 03:57:31: 8000000 INFO @ Tue, 30 Jun 2020 03:57:31: 4000000 INFO @ Tue, 30 Jun 2020 03:57:36: 13000000 INFO @ Tue, 30 Jun 2020 03:57:38: 9000000 INFO @ Tue, 30 Jun 2020 03:57:39: 5000000 INFO @ Tue, 30 Jun 2020 03:57:43: 14000000 INFO @ Tue, 30 Jun 2020 03:57:46: 10000000 INFO @ Tue, 30 Jun 2020 03:57:47: 6000000 INFO @ Tue, 30 Jun 2020 03:57:51: 15000000 INFO @ Tue, 30 Jun 2020 03:57:54: 11000000 INFO @ Tue, 30 Jun 2020 03:57:55: 7000000 INFO @ Tue, 30 Jun 2020 03:57:59: 16000000 INFO @ Tue, 30 Jun 2020 03:58:02: 12000000 INFO @ Tue, 30 Jun 2020 03:58:03: 8000000 INFO @ Tue, 30 Jun 2020 03:58:07: 17000000 INFO @ Tue, 30 Jun 2020 03:58:10: 13000000 INFO @ Tue, 30 Jun 2020 03:58:11: 9000000 INFO @ Tue, 30 Jun 2020 03:58:14: 18000000 INFO @ Tue, 30 Jun 2020 03:58:18: 14000000 INFO @ Tue, 30 Jun 2020 03:58:19: 10000000 INFO @ Tue, 30 Jun 2020 03:58:22: 19000000 INFO @ Tue, 30 Jun 2020 03:58:26: 15000000 INFO @ Tue, 30 Jun 2020 03:58:28: 11000000 INFO @ Tue, 30 Jun 2020 03:58:29: 20000000 INFO @ Tue, 30 Jun 2020 03:58:33: 16000000 INFO @ Tue, 30 Jun 2020 03:58:36: 12000000 INFO @ Tue, 30 Jun 2020 03:58:37: 21000000 INFO @ Tue, 30 Jun 2020 03:58:41: 17000000 INFO @ Tue, 30 Jun 2020 03:58:44: 13000000 INFO @ Tue, 30 Jun 2020 03:58:45: 22000000 INFO @ Tue, 30 Jun 2020 03:58:49: 18000000 INFO @ Tue, 30 Jun 2020 03:58:52: 14000000 INFO @ Tue, 30 Jun 2020 03:58:53: 23000000 INFO @ Tue, 30 Jun 2020 03:58:57: 19000000 INFO @ Tue, 30 Jun 2020 03:59:00: 15000000 INFO @ Tue, 30 Jun 2020 03:59:00: 24000000 INFO @ Tue, 30 Jun 2020 03:59:05: 20000000 INFO @ Tue, 30 Jun 2020 03:59:08: 16000000 INFO @ Tue, 30 Jun 2020 03:59:08: 25000000 INFO @ Tue, 30 Jun 2020 03:59:12: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:59:16: 26000000 INFO @ Tue, 30 Jun 2020 03:59:16: 17000000 INFO @ Tue, 30 Jun 2020 03:59:20: 22000000 INFO @ Tue, 30 Jun 2020 03:59:23: 27000000 INFO @ Tue, 30 Jun 2020 03:59:24: 18000000 INFO @ Tue, 30 Jun 2020 03:59:29: 23000000 INFO @ Tue, 30 Jun 2020 03:59:31: 28000000 INFO @ Tue, 30 Jun 2020 03:59:32: 19000000 INFO @ Tue, 30 Jun 2020 03:59:36: 24000000 INFO @ Tue, 30 Jun 2020 03:59:36: #1 tag size is determined as 67 bps INFO @ Tue, 30 Jun 2020 03:59:36: #1 tag size = 67 INFO @ Tue, 30 Jun 2020 03:59:36: #1 total tags in treatment: 28681026 INFO @ Tue, 30 Jun 2020 03:59:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:59:36: #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 03:59:37: #1 tags after filtering in treatment: 28681026 INFO @ Tue, 30 Jun 2020 03:59:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:59:37: #1 finished! INFO @ Tue, 30 Jun 2020 03:59:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:59:39: #2 number of paired peaks: 799 WARNING @ Tue, 30 Jun 2020 03:59:39: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Tue, 30 Jun 2020 03:59:39: start model_add_line... INFO @ Tue, 30 Jun 2020 03:59:39: start X-correlation... INFO @ Tue, 30 Jun 2020 03:59:39: end of X-cor INFO @ Tue, 30 Jun 2020 03:59:39: #2 finished! INFO @ Tue, 30 Jun 2020 03:59:39: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 03:59:39: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 03:59:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.05_model.r WARNING @ Tue, 30 Jun 2020 03:59:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:59:39: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 03:59:39: #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 03:59:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:59:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:59:40: 20000000 INFO @ Tue, 30 Jun 2020 03:59:44: 25000000 INFO @ Tue, 30 Jun 2020 03:59:48: 21000000 INFO @ Tue, 30 Jun 2020 03:59:52: 26000000 INFO @ Tue, 30 Jun 2020 03:59:55: 22000000 INFO @ Tue, 30 Jun 2020 03:59:59: 27000000 INFO @ Tue, 30 Jun 2020 04:00:04: 23000000 INFO @ Tue, 30 Jun 2020 04:00:07: 28000000 INFO @ Tue, 30 Jun 2020 04:00:12: 24000000 INFO @ Tue, 30 Jun 2020 04:00:12: #1 tag size is determined as 67 bps INFO @ Tue, 30 Jun 2020 04:00:12: #1 tag size = 67 INFO @ Tue, 30 Jun 2020 04:00:12: #1 total tags in treatment: 28681026 INFO @ Tue, 30 Jun 2020 04:00:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 04:00:12: #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 04:00:13: #1 tags after filtering in treatment: 28681026 INFO @ Tue, 30 Jun 2020 04:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 04:00:13: #1 finished! INFO @ Tue, 30 Jun 2020 04:00:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 04:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 04:00:15: #2 number of paired peaks: 799 WARNING @ Tue, 30 Jun 2020 04:00:15: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Tue, 30 Jun 2020 04:00:15: start model_add_line... INFO @ Tue, 30 Jun 2020 04:00:15: start X-correlation... INFO @ Tue, 30 Jun 2020 04:00:15: end of X-cor INFO @ Tue, 30 Jun 2020 04:00:15: #2 finished! INFO @ Tue, 30 Jun 2020 04:00:15: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 04:00:15: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 04:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.10_model.r WARNING @ Tue, 30 Jun 2020 04:00:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 04:00:15: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 04:00:15: #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 04:00:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 04:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 04:00:19: 25000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 04:00:26: 26000000 INFO @ Tue, 30 Jun 2020 04:00:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 04:00:34: 27000000 INFO @ Tue, 30 Jun 2020 04:00:41: 28000000 INFO @ Tue, 30 Jun 2020 04:00:46: #1 tag size is determined as 67 bps INFO @ Tue, 30 Jun 2020 04:00:46: #1 tag size = 67 INFO @ Tue, 30 Jun 2020 04:00:46: #1 total tags in treatment: 28681026 INFO @ Tue, 30 Jun 2020 04:00:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 04:00:46: #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 04:00:47: #1 tags after filtering in treatment: 28681026 INFO @ Tue, 30 Jun 2020 04:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 04:00:47: #1 finished! INFO @ Tue, 30 Jun 2020 04:00:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 04:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 04:00:49: #2 number of paired peaks: 799 WARNING @ Tue, 30 Jun 2020 04:00:49: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Tue, 30 Jun 2020 04:00:49: start model_add_line... INFO @ Tue, 30 Jun 2020 04:00:49: start X-correlation... INFO @ Tue, 30 Jun 2020 04:00:49: end of X-cor INFO @ Tue, 30 Jun 2020 04:00:49: #2 finished! INFO @ Tue, 30 Jun 2020 04:00:49: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 04:00:49: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 04:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.20_model.r WARNING @ Tue, 30 Jun 2020 04:00:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 04:00:49: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 04:00:49: #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 04:00:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 04:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 04:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.05_peaks.xls INFO @ Tue, 30 Jun 2020 04:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 04:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.05_summits.bed INFO @ Tue, 30 Jun 2020 04:00:52: Done! pass1 - making usageList (1021 chroms): 2 millis pass2 - checking and writing primary data (4537 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 04:01:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 04:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.10_peaks.xls INFO @ Tue, 30 Jun 2020 04:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 04:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.10_summits.bed INFO @ Tue, 30 Jun 2020 04:01:32: Done! pass1 - making usageList (788 chroms): 1 millis pass2 - checking and writing primary data (2857 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 04:01:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 04:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.20_peaks.xls INFO @ Tue, 30 Jun 2020 04:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 04:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750084/SRX750084.20_summits.bed INFO @ Tue, 30 Jun 2020 04:02:08: Done! pass1 - making usageList (613 chroms): 2 millis pass2 - checking and writing primary data (1997 records, 4 fields): 18 millis CompletedMACS2peakCalling