Job ID = 6529552 SRX = SRX3159475 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: 00:14:05 44918949 reads; of these: 44918949 (100.00%) were unpaired; of these: 1373869 (3.06%) aligned 0 times 30716824 (68.38%) aligned exactly 1 time 12828256 (28.56%) aligned >1 times 96.94% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 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 20 files... [bam_rmdupse_core] 7945324 / 43545080 = 0.1825 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 02:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.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 02:46:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:20: 1000000 INFO @ Tue, 30 Jun 2020 02:46:27: 2000000 INFO @ Tue, 30 Jun 2020 02:46:35: 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 02:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.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 02:46:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:43: 4000000 INFO @ Tue, 30 Jun 2020 02:46:50: 1000000 INFO @ Tue, 30 Jun 2020 02:46:52: 5000000 INFO @ Tue, 30 Jun 2020 02:46:58: 2000000 INFO @ Tue, 30 Jun 2020 02:47:01: 6000000 INFO @ Tue, 30 Jun 2020 02:47:07: 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 02:47:10: 7000000 INFO @ Tue, 30 Jun 2020 02:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.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 02:47:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:15: 4000000 INFO @ Tue, 30 Jun 2020 02:47:19: 8000000 INFO @ Tue, 30 Jun 2020 02:47:21: 1000000 INFO @ Tue, 30 Jun 2020 02:47:23: 5000000 INFO @ Tue, 30 Jun 2020 02:47:27: 9000000 INFO @ Tue, 30 Jun 2020 02:47:29: 2000000 INFO @ Tue, 30 Jun 2020 02:47:32: 6000000 INFO @ Tue, 30 Jun 2020 02:47:36: 10000000 INFO @ Tue, 30 Jun 2020 02:47:38: 3000000 INFO @ Tue, 30 Jun 2020 02:47:40: 7000000 INFO @ Tue, 30 Jun 2020 02:47:45: 11000000 INFO @ Tue, 30 Jun 2020 02:47:46: 4000000 INFO @ Tue, 30 Jun 2020 02:47:49: 8000000 INFO @ Tue, 30 Jun 2020 02:47:53: 12000000 INFO @ Tue, 30 Jun 2020 02:47:54: 5000000 INFO @ Tue, 30 Jun 2020 02:47:57: 9000000 INFO @ Tue, 30 Jun 2020 02:48:02: 13000000 INFO @ Tue, 30 Jun 2020 02:48:03: 6000000 INFO @ Tue, 30 Jun 2020 02:48:05: 10000000 INFO @ Tue, 30 Jun 2020 02:48:11: 14000000 INFO @ Tue, 30 Jun 2020 02:48:11: 7000000 INFO @ Tue, 30 Jun 2020 02:48:13: 11000000 INFO @ Tue, 30 Jun 2020 02:48:19: 8000000 INFO @ Tue, 30 Jun 2020 02:48:20: 15000000 INFO @ Tue, 30 Jun 2020 02:48:22: 12000000 INFO @ Tue, 30 Jun 2020 02:48:27: 9000000 INFO @ Tue, 30 Jun 2020 02:48:29: 16000000 INFO @ Tue, 30 Jun 2020 02:48:30: 13000000 INFO @ Tue, 30 Jun 2020 02:48:35: 10000000 INFO @ Tue, 30 Jun 2020 02:48:37: 17000000 INFO @ Tue, 30 Jun 2020 02:48:38: 14000000 INFO @ Tue, 30 Jun 2020 02:48:43: 11000000 INFO @ Tue, 30 Jun 2020 02:48:46: 15000000 INFO @ Tue, 30 Jun 2020 02:48:46: 18000000 INFO @ Tue, 30 Jun 2020 02:48:51: 12000000 INFO @ Tue, 30 Jun 2020 02:48:54: 16000000 INFO @ Tue, 30 Jun 2020 02:48:55: 19000000 INFO @ Tue, 30 Jun 2020 02:48:59: 13000000 INFO @ Tue, 30 Jun 2020 02:49:02: 17000000 INFO @ Tue, 30 Jun 2020 02:49:04: 20000000 INFO @ Tue, 30 Jun 2020 02:49:07: 14000000 INFO @ Tue, 30 Jun 2020 02:49:09: 18000000 INFO @ Tue, 30 Jun 2020 02:49:13: 21000000 INFO @ Tue, 30 Jun 2020 02:49:15: 15000000 INFO @ Tue, 30 Jun 2020 02:49:17: 19000000 INFO @ Tue, 30 Jun 2020 02:49:21: 22000000 INFO @ Tue, 30 Jun 2020 02:49:23: 16000000 INFO @ Tue, 30 Jun 2020 02:49:26: 20000000 INFO @ Tue, 30 Jun 2020 02:49:30: 23000000 INFO @ Tue, 30 Jun 2020 02:49:31: 17000000 INFO @ Tue, 30 Jun 2020 02:49:34: 21000000 INFO @ Tue, 30 Jun 2020 02:49:38: 24000000 INFO @ Tue, 30 Jun 2020 02:49:39: 18000000 INFO @ Tue, 30 Jun 2020 02:49:42: 22000000 INFO @ Tue, 30 Jun 2020 02:49:47: 25000000 INFO @ Tue, 30 Jun 2020 02:49:47: 19000000 INFO @ Tue, 30 Jun 2020 02:49:50: 23000000 INFO @ Tue, 30 Jun 2020 02:49:55: 26000000 INFO @ Tue, 30 Jun 2020 02:49:56: 20000000 INFO @ Tue, 30 Jun 2020 02:49:58: 24000000 INFO @ Tue, 30 Jun 2020 02:50:03: 27000000 INFO @ Tue, 30 Jun 2020 02:50:04: 21000000 INFO @ Tue, 30 Jun 2020 02:50:07: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:50:12: 28000000 INFO @ Tue, 30 Jun 2020 02:50:13: 22000000 INFO @ Tue, 30 Jun 2020 02:50:15: 26000000 INFO @ Tue, 30 Jun 2020 02:50:21: 23000000 INFO @ Tue, 30 Jun 2020 02:50:21: 29000000 INFO @ Tue, 30 Jun 2020 02:50:23: 27000000 INFO @ Tue, 30 Jun 2020 02:50:29: 24000000 INFO @ Tue, 30 Jun 2020 02:50:29: 30000000 INFO @ Tue, 30 Jun 2020 02:50:31: 28000000 INFO @ Tue, 30 Jun 2020 02:50:37: 25000000 INFO @ Tue, 30 Jun 2020 02:50:38: 31000000 INFO @ Tue, 30 Jun 2020 02:50:40: 29000000 INFO @ Tue, 30 Jun 2020 02:50:45: 26000000 INFO @ Tue, 30 Jun 2020 02:50:46: 32000000 INFO @ Tue, 30 Jun 2020 02:50:48: 30000000 INFO @ Tue, 30 Jun 2020 02:50:53: 27000000 INFO @ Tue, 30 Jun 2020 02:50:54: 33000000 INFO @ Tue, 30 Jun 2020 02:50:56: 31000000 INFO @ Tue, 30 Jun 2020 02:51:01: 28000000 INFO @ Tue, 30 Jun 2020 02:51:03: 34000000 INFO @ Tue, 30 Jun 2020 02:51:04: 32000000 INFO @ Tue, 30 Jun 2020 02:51:10: 29000000 INFO @ Tue, 30 Jun 2020 02:51:12: 35000000 INFO @ Tue, 30 Jun 2020 02:51:12: 33000000 INFO @ Tue, 30 Jun 2020 02:51:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:51:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:51:17: #1 total tags in treatment: 35599756 INFO @ Tue, 30 Jun 2020 02:51:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:17: #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 02:51:18: 30000000 INFO @ Tue, 30 Jun 2020 02:51:18: #1 tags after filtering in treatment: 35599756 INFO @ Tue, 30 Jun 2020 02:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:20: 34000000 INFO @ Tue, 30 Jun 2020 02:51:20: #2 number of paired peaks: 132 WARNING @ Tue, 30 Jun 2020 02:51:20: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:20: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:51:20: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 02:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.05_model.r WARNING @ Tue, 30 Jun 2020 02:51:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:20: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 02:51:20: #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 02:51:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:25: 31000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:51:27: 35000000 INFO @ Tue, 30 Jun 2020 02:51:31: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:51:31: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:51:31: #1 total tags in treatment: 35599756 INFO @ Tue, 30 Jun 2020 02:51:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:31: #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 02:51:32: 32000000 INFO @ Tue, 30 Jun 2020 02:51:32: #1 tags after filtering in treatment: 35599756 INFO @ Tue, 30 Jun 2020 02:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:35: #2 number of paired peaks: 132 WARNING @ Tue, 30 Jun 2020 02:51:35: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:35: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:51:35: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 02:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.10_model.r WARNING @ Tue, 30 Jun 2020 02:51:35: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:35: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 02:51:35: #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 02:51:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:38: 33000000 INFO @ Tue, 30 Jun 2020 02:51:45: 34000000 INFO @ Tue, 30 Jun 2020 02:51:52: 35000000 INFO @ Tue, 30 Jun 2020 02:51:56: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:51:56: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:51:56: #1 total tags in treatment: 35599756 INFO @ Tue, 30 Jun 2020 02:51:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:56: #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 02:51:57: #1 tags after filtering in treatment: 35599756 INFO @ Tue, 30 Jun 2020 02:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:59: #2 number of paired peaks: 132 WARNING @ Tue, 30 Jun 2020 02:51:59: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:59: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:51:59: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 02:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.20_model.r WARNING @ Tue, 30 Jun 2020 02:51:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:59: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 02:51:59: #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 02:51:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.05_summits.bed INFO @ Tue, 30 Jun 2020 02:52:50: Done! pass1 - making usageList (761 chroms): 1 millis pass2 - checking and writing primary data (3332 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.10_summits.bed INFO @ Tue, 30 Jun 2020 02:53:09: Done! pass1 - making usageList (642 chroms): 2 millis pass2 - checking and writing primary data (2492 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159475/SRX3159475.20_summits.bed INFO @ Tue, 30 Jun 2020 02:53:33: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (1137 records, 4 fields): 15 millis CompletedMACS2peakCalling