Job ID = 6529555 SRX = SRX3159484 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: 00:13:30 42389119 reads; of these: 42389119 (100.00%) were unpaired; of these: 1120099 (2.64%) aligned 0 times 29076164 (68.59%) aligned exactly 1 time 12192856 (28.76%) aligned >1 times 97.36% overall alignment rate Time searching: 00:13:30 Overall time: 00:13:30 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 20 files... [bam_rmdupse_core] 8155457 / 41269020 = 0.1976 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 02:58:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.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 02:58:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:21: 1000000 INFO @ Tue, 30 Jun 2020 02:58:29: 2000000 INFO @ Tue, 30 Jun 2020 02:58:38: 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 02:58:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.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 02:58:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:46: 4000000 INFO @ Tue, 30 Jun 2020 02:58:51: 1000000 INFO @ Tue, 30 Jun 2020 02:58:54: 5000000 INFO @ Tue, 30 Jun 2020 02:58:59: 2000000 INFO @ Tue, 30 Jun 2020 02:59:03: 6000000 INFO @ Tue, 30 Jun 2020 02:59:07: 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 02:59:11: 7000000 INFO @ Tue, 30 Jun 2020 02:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.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 02:59:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:16: 4000000 INFO @ Tue, 30 Jun 2020 02:59:19: 1000000 INFO @ Tue, 30 Jun 2020 02:59:20: 8000000 INFO @ Tue, 30 Jun 2020 02:59:24: 5000000 INFO @ Tue, 30 Jun 2020 02:59:25: 2000000 INFO @ Tue, 30 Jun 2020 02:59:28: 9000000 INFO @ Tue, 30 Jun 2020 02:59:32: 3000000 INFO @ Tue, 30 Jun 2020 02:59:33: 6000000 INFO @ Tue, 30 Jun 2020 02:59:37: 10000000 INFO @ Tue, 30 Jun 2020 02:59:38: 4000000 INFO @ Tue, 30 Jun 2020 02:59:42: 7000000 INFO @ Tue, 30 Jun 2020 02:59:44: 5000000 INFO @ Tue, 30 Jun 2020 02:59:45: 11000000 INFO @ Tue, 30 Jun 2020 02:59:50: 8000000 INFO @ Tue, 30 Jun 2020 02:59:51: 6000000 INFO @ Tue, 30 Jun 2020 02:59:54: 12000000 INFO @ Tue, 30 Jun 2020 02:59:57: 7000000 INFO @ Tue, 30 Jun 2020 02:59:59: 9000000 INFO @ Tue, 30 Jun 2020 03:00:02: 13000000 INFO @ Tue, 30 Jun 2020 03:00:03: 8000000 INFO @ Tue, 30 Jun 2020 03:00:07: 10000000 INFO @ Tue, 30 Jun 2020 03:00:09: 9000000 INFO @ Tue, 30 Jun 2020 03:00:11: 14000000 INFO @ Tue, 30 Jun 2020 03:00:16: 11000000 INFO @ Tue, 30 Jun 2020 03:00:16: 10000000 INFO @ Tue, 30 Jun 2020 03:00:19: 15000000 INFO @ Tue, 30 Jun 2020 03:00:23: 11000000 INFO @ Tue, 30 Jun 2020 03:00:24: 12000000 INFO @ Tue, 30 Jun 2020 03:00:28: 16000000 INFO @ Tue, 30 Jun 2020 03:00:29: 12000000 INFO @ Tue, 30 Jun 2020 03:00:33: 13000000 INFO @ Tue, 30 Jun 2020 03:00:35: 13000000 INFO @ Tue, 30 Jun 2020 03:00:36: 17000000 INFO @ Tue, 30 Jun 2020 03:00:41: 14000000 INFO @ Tue, 30 Jun 2020 03:00:41: 14000000 INFO @ Tue, 30 Jun 2020 03:00:45: 18000000 INFO @ Tue, 30 Jun 2020 03:00:48: 15000000 INFO @ Tue, 30 Jun 2020 03:00:50: 15000000 INFO @ Tue, 30 Jun 2020 03:00:53: 19000000 INFO @ Tue, 30 Jun 2020 03:00:55: 16000000 INFO @ Tue, 30 Jun 2020 03:00:58: 16000000 INFO @ Tue, 30 Jun 2020 03:01:01: 17000000 INFO @ Tue, 30 Jun 2020 03:01:01: 20000000 INFO @ Tue, 30 Jun 2020 03:01:06: 17000000 INFO @ Tue, 30 Jun 2020 03:01:07: 18000000 INFO @ Tue, 30 Jun 2020 03:01:09: 21000000 INFO @ Tue, 30 Jun 2020 03:01:14: 19000000 INFO @ Tue, 30 Jun 2020 03:01:14: 18000000 INFO @ Tue, 30 Jun 2020 03:01:17: 22000000 INFO @ Tue, 30 Jun 2020 03:01:20: 20000000 INFO @ Tue, 30 Jun 2020 03:01:22: 19000000 INFO @ Tue, 30 Jun 2020 03:01:25: 23000000 INFO @ Tue, 30 Jun 2020 03:01:26: 21000000 INFO @ Tue, 30 Jun 2020 03:01:30: 20000000 INFO @ Tue, 30 Jun 2020 03:01:32: 22000000 INFO @ Tue, 30 Jun 2020 03:01:33: 24000000 INFO @ Tue, 30 Jun 2020 03:01:38: 21000000 INFO @ Tue, 30 Jun 2020 03:01:38: 23000000 INFO @ Tue, 30 Jun 2020 03:01:42: 25000000 INFO @ Tue, 30 Jun 2020 03:01:44: 24000000 INFO @ Tue, 30 Jun 2020 03:01:46: 22000000 INFO @ Tue, 30 Jun 2020 03:01:50: 26000000 INFO @ Tue, 30 Jun 2020 03:01:51: 25000000 INFO @ Tue, 30 Jun 2020 03:01:55: 23000000 INFO @ Tue, 30 Jun 2020 03:01:57: 26000000 INFO @ Tue, 30 Jun 2020 03:01:59: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:02:03: 24000000 INFO @ Tue, 30 Jun 2020 03:02:05: 27000000 INFO @ Tue, 30 Jun 2020 03:02:07: 28000000 INFO @ Tue, 30 Jun 2020 03:02:11: 25000000 INFO @ Tue, 30 Jun 2020 03:02:11: 28000000 INFO @ Tue, 30 Jun 2020 03:02:15: 29000000 INFO @ Tue, 30 Jun 2020 03:02:17: 29000000 INFO @ Tue, 30 Jun 2020 03:02:19: 26000000 INFO @ Tue, 30 Jun 2020 03:02:23: 30000000 INFO @ Tue, 30 Jun 2020 03:02:23: 30000000 INFO @ Tue, 30 Jun 2020 03:02:28: 27000000 INFO @ Tue, 30 Jun 2020 03:02:30: 31000000 INFO @ Tue, 30 Jun 2020 03:02:31: 31000000 INFO @ Tue, 30 Jun 2020 03:02:36: 28000000 INFO @ Tue, 30 Jun 2020 03:02:36: 32000000 INFO @ Tue, 30 Jun 2020 03:02:39: 32000000 INFO @ Tue, 30 Jun 2020 03:02:43: 33000000 INFO @ Tue, 30 Jun 2020 03:02:44: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:02:44: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:02:44: #1 total tags in treatment: 33113563 INFO @ Tue, 30 Jun 2020 03:02:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:02:44: #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 03:02:44: 29000000 INFO @ Tue, 30 Jun 2020 03:02:45: #1 tags after filtering in treatment: 33113562 INFO @ Tue, 30 Jun 2020 03:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:02:45: #1 finished! INFO @ Tue, 30 Jun 2020 03:02:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:02:47: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 03:02:47: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 03:02:47: start model_add_line... INFO @ Tue, 30 Jun 2020 03:02:47: start X-correlation... INFO @ Tue, 30 Jun 2020 03:02:47: end of X-cor INFO @ Tue, 30 Jun 2020 03:02:47: #2 finished! INFO @ Tue, 30 Jun 2020 03:02:47: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:02:47: #2 alternative fragment length(s) may be 1,50,573,592 bps INFO @ Tue, 30 Jun 2020 03:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.20_model.r WARNING @ Tue, 30 Jun 2020 03:02:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:02:47: #2 You may need to consider one of the other alternative d(s): 1,50,573,592 WARNING @ Tue, 30 Jun 2020 03:02:47: #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 03:02:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:02:47: 33000000 INFO @ Tue, 30 Jun 2020 03:02:48: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:02:48: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:02:48: #1 total tags in treatment: 33113563 INFO @ Tue, 30 Jun 2020 03:02:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:02:48: #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 03:02:50: #1 tags after filtering in treatment: 33113562 INFO @ Tue, 30 Jun 2020 03:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:02:50: #1 finished! INFO @ Tue, 30 Jun 2020 03:02:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:02:51: 30000000 INFO @ Tue, 30 Jun 2020 03:02:52: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 03:02:52: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 03:02:52: start model_add_line... INFO @ Tue, 30 Jun 2020 03:02:52: start X-correlation... INFO @ Tue, 30 Jun 2020 03:02:52: end of X-cor INFO @ Tue, 30 Jun 2020 03:02:52: #2 finished! INFO @ Tue, 30 Jun 2020 03:02:52: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:02:52: #2 alternative fragment length(s) may be 1,50,573,592 bps INFO @ Tue, 30 Jun 2020 03:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.05_model.r WARNING @ Tue, 30 Jun 2020 03:02:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:02:52: #2 You may need to consider one of the other alternative d(s): 1,50,573,592 WARNING @ Tue, 30 Jun 2020 03:02:52: #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 03:02:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:02:59: 31000000 INFO @ Tue, 30 Jun 2020 03:03:06: 32000000 INFO @ Tue, 30 Jun 2020 03:03:14: 33000000 INFO @ Tue, 30 Jun 2020 03:03:15: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:03:15: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:03:15: #1 total tags in treatment: 33113563 INFO @ Tue, 30 Jun 2020 03:03:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:03:15: #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 03:03:16: #1 tags after filtering in treatment: 33113562 INFO @ Tue, 30 Jun 2020 03:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:03:16: #1 finished! INFO @ Tue, 30 Jun 2020 03:03:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:03:18: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 03:03:18: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 03:03:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:03:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:03:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:03:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:03:18: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:03:18: #2 alternative fragment length(s) may be 1,50,573,592 bps INFO @ Tue, 30 Jun 2020 03:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.10_model.r WARNING @ Tue, 30 Jun 2020 03:03:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:03:19: #2 You may need to consider one of the other alternative d(s): 1,50,573,592 WARNING @ Tue, 30 Jun 2020 03:03:19: #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 03:03:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:03:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:03:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:03:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:04:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.20_summits.bed INFO @ Tue, 30 Jun 2020 03:04:03: Done! pass1 - making usageList (404 chroms): 1 millis pass2 - checking and writing primary data (983 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.05_summits.bed INFO @ Tue, 30 Jun 2020 03:04:09: Done! pass1 - making usageList (831 chroms): 2 millis pass2 - checking and writing primary data (4302 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:04:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:04:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159484/SRX3159484.10_summits.bed INFO @ Tue, 30 Jun 2020 03:04:36: Done! pass1 - making usageList (676 chroms): 2 millis pass2 - checking and writing primary data (2719 records, 4 fields): 39 millis CompletedMACS2peakCalling