Job ID = 6530101 SRX = SRX969910 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: 00:10:30 43236646 reads; of these: 43236646 (100.00%) were unpaired; of these: 6404847 (14.81%) aligned 0 times 29189110 (67.51%) aligned exactly 1 time 7642689 (17.68%) aligned >1 times 85.19% overall alignment rate Time searching: 00:10:30 Overall time: 00:10:30 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] 6382093 / 36831799 = 0.1733 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 03:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.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 03:38:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:38:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:38:15: 1000000 INFO @ Tue, 30 Jun 2020 03:38:21: 2000000 INFO @ Tue, 30 Jun 2020 03:38:28: 3000000 INFO @ Tue, 30 Jun 2020 03:38:35: 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 03:38:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.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 03:38:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:38:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:38:41: 5000000 INFO @ Tue, 30 Jun 2020 03:38:45: 1000000 INFO @ Tue, 30 Jun 2020 03:38:49: 6000000 INFO @ Tue, 30 Jun 2020 03:38:52: 2000000 INFO @ Tue, 30 Jun 2020 03:38:55: 7000000 INFO @ Tue, 30 Jun 2020 03:39:00: 3000000 INFO @ Tue, 30 Jun 2020 03:39:02: 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 03:39:07: 4000000 INFO @ Tue, 30 Jun 2020 03:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.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 03:39:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:39:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:39:09: 9000000 INFO @ Tue, 30 Jun 2020 03:39:15: 5000000 INFO @ Tue, 30 Jun 2020 03:39:15: 1000000 INFO @ Tue, 30 Jun 2020 03:39:17: 10000000 INFO @ Tue, 30 Jun 2020 03:39:22: 2000000 INFO @ Tue, 30 Jun 2020 03:39:22: 6000000 INFO @ Tue, 30 Jun 2020 03:39:24: 11000000 INFO @ Tue, 30 Jun 2020 03:39:30: 3000000 INFO @ Tue, 30 Jun 2020 03:39:30: 7000000 INFO @ Tue, 30 Jun 2020 03:39:31: 12000000 INFO @ Tue, 30 Jun 2020 03:39:37: 4000000 INFO @ Tue, 30 Jun 2020 03:39:38: 8000000 INFO @ Tue, 30 Jun 2020 03:39:39: 13000000 INFO @ Tue, 30 Jun 2020 03:39:44: 5000000 INFO @ Tue, 30 Jun 2020 03:39:45: 9000000 INFO @ Tue, 30 Jun 2020 03:39:46: 14000000 INFO @ Tue, 30 Jun 2020 03:39:52: 6000000 INFO @ Tue, 30 Jun 2020 03:39:53: 10000000 INFO @ Tue, 30 Jun 2020 03:39:53: 15000000 INFO @ Tue, 30 Jun 2020 03:39:59: 7000000 INFO @ Tue, 30 Jun 2020 03:40:01: 16000000 INFO @ Tue, 30 Jun 2020 03:40:01: 11000000 INFO @ Tue, 30 Jun 2020 03:40:06: 8000000 INFO @ Tue, 30 Jun 2020 03:40:08: 17000000 INFO @ Tue, 30 Jun 2020 03:40:09: 12000000 INFO @ Tue, 30 Jun 2020 03:40:14: 9000000 INFO @ Tue, 30 Jun 2020 03:40:15: 18000000 INFO @ Tue, 30 Jun 2020 03:40:16: 13000000 INFO @ Tue, 30 Jun 2020 03:40:21: 10000000 INFO @ Tue, 30 Jun 2020 03:40:23: 19000000 INFO @ Tue, 30 Jun 2020 03:40:24: 14000000 INFO @ Tue, 30 Jun 2020 03:40:28: 11000000 INFO @ Tue, 30 Jun 2020 03:40:30: 20000000 INFO @ Tue, 30 Jun 2020 03:40:32: 15000000 INFO @ Tue, 30 Jun 2020 03:40:36: 12000000 INFO @ Tue, 30 Jun 2020 03:40:37: 21000000 INFO @ Tue, 30 Jun 2020 03:40:39: 16000000 INFO @ Tue, 30 Jun 2020 03:40:43: 13000000 INFO @ Tue, 30 Jun 2020 03:40:44: 22000000 INFO @ Tue, 30 Jun 2020 03:40:47: 17000000 INFO @ Tue, 30 Jun 2020 03:40:50: 14000000 INFO @ Tue, 30 Jun 2020 03:40:51: 23000000 INFO @ Tue, 30 Jun 2020 03:40:55: 18000000 INFO @ Tue, 30 Jun 2020 03:40:57: 15000000 INFO @ Tue, 30 Jun 2020 03:40:58: 24000000 INFO @ Tue, 30 Jun 2020 03:41:02: 19000000 INFO @ Tue, 30 Jun 2020 03:41:04: 16000000 INFO @ Tue, 30 Jun 2020 03:41:05: 25000000 INFO @ Tue, 30 Jun 2020 03:41:10: 20000000 INFO @ Tue, 30 Jun 2020 03:41:12: 17000000 INFO @ Tue, 30 Jun 2020 03:41:13: 26000000 INFO @ Tue, 30 Jun 2020 03:41:17: 21000000 INFO @ Tue, 30 Jun 2020 03:41:19: 18000000 INFO @ Tue, 30 Jun 2020 03:41:20: 27000000 INFO @ Tue, 30 Jun 2020 03:41:25: 22000000 INFO @ Tue, 30 Jun 2020 03:41:26: 19000000 INFO @ Tue, 30 Jun 2020 03:41:28: 28000000 INFO @ Tue, 30 Jun 2020 03:41:32: 23000000 INFO @ Tue, 30 Jun 2020 03:41:33: 20000000 INFO @ Tue, 30 Jun 2020 03:41:35: 29000000 INFO @ Tue, 30 Jun 2020 03:41:40: 24000000 INFO @ Tue, 30 Jun 2020 03:41:41: 21000000 INFO @ Tue, 30 Jun 2020 03:41:42: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:41:46: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:41:46: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:41:46: #1 total tags in treatment: 30449706 INFO @ Tue, 30 Jun 2020 03:41:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:41:46: #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 03:41:47: #1 tags after filtering in treatment: 30449699 INFO @ Tue, 30 Jun 2020 03:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:41:47: #1 finished! INFO @ Tue, 30 Jun 2020 03:41:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:41:48: 25000000 INFO @ Tue, 30 Jun 2020 03:41:48: 22000000 INFO @ Tue, 30 Jun 2020 03:41:49: #2 number of paired peaks: 158 WARNING @ Tue, 30 Jun 2020 03:41:49: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 30 Jun 2020 03:41:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:41:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:41:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:41:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:41:49: #2 predicted fragment length is 92 bps INFO @ Tue, 30 Jun 2020 03:41:49: #2 alternative fragment length(s) may be 3,92 bps INFO @ Tue, 30 Jun 2020 03:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.05_model.r WARNING @ Tue, 30 Jun 2020 03:41:49: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:41:49: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Tue, 30 Jun 2020 03:41:49: #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 03:41:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:41:54: 23000000 INFO @ Tue, 30 Jun 2020 03:41:56: 26000000 INFO @ Tue, 30 Jun 2020 03:42:01: 24000000 INFO @ Tue, 30 Jun 2020 03:42:03: 27000000 INFO @ Tue, 30 Jun 2020 03:42:08: 25000000 INFO @ Tue, 30 Jun 2020 03:42:11: 28000000 INFO @ Tue, 30 Jun 2020 03:42:15: 26000000 INFO @ Tue, 30 Jun 2020 03:42:18: 29000000 INFO @ Tue, 30 Jun 2020 03:42:22: 27000000 INFO @ Tue, 30 Jun 2020 03:42:26: 30000000 INFO @ Tue, 30 Jun 2020 03:42:29: 28000000 INFO @ Tue, 30 Jun 2020 03:42:30: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:42:30: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:42:30: #1 total tags in treatment: 30449706 INFO @ Tue, 30 Jun 2020 03:42:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:42:30: #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 03:42:31: #1 tags after filtering in treatment: 30449699 INFO @ Tue, 30 Jun 2020 03:42:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:42:31: #1 finished! INFO @ Tue, 30 Jun 2020 03:42:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:42:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:42:33: #2 number of paired peaks: 158 WARNING @ Tue, 30 Jun 2020 03:42:33: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 30 Jun 2020 03:42:33: start model_add_line... INFO @ Tue, 30 Jun 2020 03:42:33: start X-correlation... INFO @ Tue, 30 Jun 2020 03:42:33: end of X-cor INFO @ Tue, 30 Jun 2020 03:42:33: #2 finished! INFO @ Tue, 30 Jun 2020 03:42:33: #2 predicted fragment length is 92 bps INFO @ Tue, 30 Jun 2020 03:42:33: #2 alternative fragment length(s) may be 3,92 bps INFO @ Tue, 30 Jun 2020 03:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.10_model.r WARNING @ Tue, 30 Jun 2020 03:42:33: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:42:33: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Tue, 30 Jun 2020 03:42:33: #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 03:42:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:42:35: 29000000 INFO @ Tue, 30 Jun 2020 03:42:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:42:42: 30000000 INFO @ Tue, 30 Jun 2020 03:42:46: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:42:46: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:42:46: #1 total tags in treatment: 30449706 INFO @ Tue, 30 Jun 2020 03:42:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:42:46: #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 03:42:47: #1 tags after filtering in treatment: 30449699 INFO @ Tue, 30 Jun 2020 03:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:42:47: #1 finished! INFO @ Tue, 30 Jun 2020 03:42:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:42:49: #2 number of paired peaks: 158 WARNING @ Tue, 30 Jun 2020 03:42:49: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 30 Jun 2020 03:42:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:42:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:42:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:42:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:42:49: #2 predicted fragment length is 92 bps INFO @ Tue, 30 Jun 2020 03:42:49: #2 alternative fragment length(s) may be 3,92 bps INFO @ Tue, 30 Jun 2020 03:42:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.20_model.r WARNING @ Tue, 30 Jun 2020 03:42:49: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:42:49: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Tue, 30 Jun 2020 03:42:49: #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 03:42:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:42:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.05_summits.bed INFO @ Tue, 30 Jun 2020 03:43:09: Done! pass1 - making usageList (380 chroms): 2 millis pass2 - checking and writing primary data (6450 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:43:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:43:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.10_summits.bed INFO @ Tue, 30 Jun 2020 03:43:55: Done! pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (3291 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969910/SRX969910.20_summits.bed INFO @ Tue, 30 Jun 2020 03:44:08: Done! pass1 - making usageList (146 chroms): 1 millis pass2 - checking and writing primary data (1287 records, 4 fields): 26 millis CompletedMACS2peakCalling