Job ID = 6529243 SRX = SRX1085379 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: 00:12:16 35038509 reads; of these: 35038509 (100.00%) were unpaired; of these: 897285 (2.56%) aligned 0 times 28612422 (81.66%) aligned exactly 1 time 5528802 (15.78%) aligned >1 times 97.44% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 4763005 / 34141224 = 0.1395 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 02:00:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.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 02:00:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:00:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:00:53: 1000000 INFO @ Tue, 30 Jun 2020 02:00:59: 2000000 INFO @ Tue, 30 Jun 2020 02:01:04: 3000000 INFO @ Tue, 30 Jun 2020 02:01:10: 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 02:01:16: 5000000 INFO @ Tue, 30 Jun 2020 02:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.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 02:01:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:22: 6000000 INFO @ Tue, 30 Jun 2020 02:01:23: 1000000 INFO @ Tue, 30 Jun 2020 02:01:28: 7000000 INFO @ Tue, 30 Jun 2020 02:01:29: 2000000 INFO @ Tue, 30 Jun 2020 02:01:35: 8000000 INFO @ Tue, 30 Jun 2020 02:01:36: 3000000 INFO @ Tue, 30 Jun 2020 02:01:41: 9000000 INFO @ Tue, 30 Jun 2020 02:01:42: 4000000 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 02:01:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.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 02:01:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:47: 10000000 INFO @ Tue, 30 Jun 2020 02:01:48: 5000000 INFO @ Tue, 30 Jun 2020 02:01:53: 1000000 INFO @ Tue, 30 Jun 2020 02:01:53: 11000000 INFO @ Tue, 30 Jun 2020 02:01:55: 6000000 INFO @ Tue, 30 Jun 2020 02:02:00: 2000000 INFO @ Tue, 30 Jun 2020 02:02:00: 12000000 INFO @ Tue, 30 Jun 2020 02:02:01: 7000000 INFO @ Tue, 30 Jun 2020 02:02:06: 3000000 INFO @ Tue, 30 Jun 2020 02:02:06: 13000000 INFO @ Tue, 30 Jun 2020 02:02:07: 8000000 INFO @ Tue, 30 Jun 2020 02:02:12: 4000000 INFO @ Tue, 30 Jun 2020 02:02:12: 14000000 INFO @ Tue, 30 Jun 2020 02:02:14: 9000000 INFO @ Tue, 30 Jun 2020 02:02:18: 5000000 INFO @ Tue, 30 Jun 2020 02:02:18: 15000000 INFO @ Tue, 30 Jun 2020 02:02:20: 10000000 INFO @ Tue, 30 Jun 2020 02:02:25: 16000000 INFO @ Tue, 30 Jun 2020 02:02:25: 6000000 INFO @ Tue, 30 Jun 2020 02:02:26: 11000000 INFO @ Tue, 30 Jun 2020 02:02:31: 7000000 INFO @ Tue, 30 Jun 2020 02:02:31: 17000000 INFO @ Tue, 30 Jun 2020 02:02:33: 12000000 INFO @ Tue, 30 Jun 2020 02:02:37: 18000000 INFO @ Tue, 30 Jun 2020 02:02:37: 8000000 INFO @ Tue, 30 Jun 2020 02:02:39: 13000000 INFO @ Tue, 30 Jun 2020 02:02:43: 19000000 INFO @ Tue, 30 Jun 2020 02:02:43: 9000000 INFO @ Tue, 30 Jun 2020 02:02:45: 14000000 INFO @ Tue, 30 Jun 2020 02:02:49: 20000000 INFO @ Tue, 30 Jun 2020 02:02:50: 10000000 INFO @ Tue, 30 Jun 2020 02:02:52: 15000000 INFO @ Tue, 30 Jun 2020 02:02:56: 21000000 INFO @ Tue, 30 Jun 2020 02:02:56: 11000000 INFO @ Tue, 30 Jun 2020 02:02:58: 16000000 INFO @ Tue, 30 Jun 2020 02:03:02: 22000000 INFO @ Tue, 30 Jun 2020 02:03:02: 12000000 INFO @ Tue, 30 Jun 2020 02:03:05: 17000000 INFO @ Tue, 30 Jun 2020 02:03:08: 23000000 INFO @ Tue, 30 Jun 2020 02:03:09: 13000000 INFO @ Tue, 30 Jun 2020 02:03:11: 18000000 INFO @ Tue, 30 Jun 2020 02:03:14: 24000000 INFO @ Tue, 30 Jun 2020 02:03:15: 14000000 INFO @ Tue, 30 Jun 2020 02:03:17: 19000000 INFO @ Tue, 30 Jun 2020 02:03:21: 25000000 INFO @ Tue, 30 Jun 2020 02:03:21: 15000000 INFO @ Tue, 30 Jun 2020 02:03:23: 20000000 INFO @ Tue, 30 Jun 2020 02:03:27: 26000000 INFO @ Tue, 30 Jun 2020 02:03:27: 16000000 INFO @ Tue, 30 Jun 2020 02:03:29: 21000000 INFO @ Tue, 30 Jun 2020 02:03:33: 27000000 INFO @ Tue, 30 Jun 2020 02:03:34: 17000000 INFO @ Tue, 30 Jun 2020 02:03:36: 22000000 INFO @ Tue, 30 Jun 2020 02:03:39: 28000000 INFO @ Tue, 30 Jun 2020 02:03:40: 18000000 INFO @ Tue, 30 Jun 2020 02:03:42: 23000000 INFO @ Tue, 30 Jun 2020 02:03:45: 29000000 INFO @ Tue, 30 Jun 2020 02:03:46: 19000000 INFO @ Tue, 30 Jun 2020 02:03:48: #1 tag size is determined as 80 bps INFO @ Tue, 30 Jun 2020 02:03:48: #1 tag size = 80 INFO @ Tue, 30 Jun 2020 02:03:48: #1 total tags in treatment: 29378219 INFO @ Tue, 30 Jun 2020 02:03:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:48: #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 02:03:48: 24000000 INFO @ Tue, 30 Jun 2020 02:03:49: #1 tags after filtering in treatment: 29378215 INFO @ Tue, 30 Jun 2020 02:03:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:50: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:03:50: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:51: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:03:51: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.05_model.r WARNING @ Tue, 30 Jun 2020 02:03:51: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:03:51: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:03:51: #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 02:03:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:52: 20000000 INFO @ Tue, 30 Jun 2020 02:03:55: 25000000 INFO @ Tue, 30 Jun 2020 02:03:58: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:04:01: 26000000 INFO @ Tue, 30 Jun 2020 02:04:04: 22000000 INFO @ Tue, 30 Jun 2020 02:04:07: 27000000 INFO @ Tue, 30 Jun 2020 02:04:10: 23000000 INFO @ Tue, 30 Jun 2020 02:04:13: 28000000 INFO @ Tue, 30 Jun 2020 02:04:17: 24000000 INFO @ Tue, 30 Jun 2020 02:04:19: 29000000 INFO @ Tue, 30 Jun 2020 02:04:22: #1 tag size is determined as 80 bps INFO @ Tue, 30 Jun 2020 02:04:22: #1 tag size = 80 INFO @ Tue, 30 Jun 2020 02:04:22: #1 total tags in treatment: 29378219 INFO @ Tue, 30 Jun 2020 02:04:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:04:22: #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 02:04:23: #1 tags after filtering in treatment: 29378215 INFO @ Tue, 30 Jun 2020 02:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:04:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:04:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:04:23: 25000000 INFO @ Tue, 30 Jun 2020 02:04:25: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:04:25: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:04:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:04:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:04:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:04:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:04:25: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:04:25: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.10_model.r WARNING @ Tue, 30 Jun 2020 02:04:25: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:04:25: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:04:25: #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 02:04:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:04:29: 26000000 INFO @ Tue, 30 Jun 2020 02:04:35: 27000000 INFO @ Tue, 30 Jun 2020 02:04:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:04:41: 28000000 INFO @ Tue, 30 Jun 2020 02:04:47: 29000000 INFO @ Tue, 30 Jun 2020 02:04:49: #1 tag size is determined as 80 bps INFO @ Tue, 30 Jun 2020 02:04:49: #1 tag size = 80 INFO @ Tue, 30 Jun 2020 02:04:49: #1 total tags in treatment: 29378219 INFO @ Tue, 30 Jun 2020 02:04:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:04:49: #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 02:04:50: #1 tags after filtering in treatment: 29378215 INFO @ Tue, 30 Jun 2020 02:04:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:04:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:04:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:04:52: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:04:52: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:04:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:04:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:04:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:04:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:04:52: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:04:52: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.20_model.r WARNING @ Tue, 30 Jun 2020 02:04:52: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:04:52: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:04:52: #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 02:04:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.05_summits.bed INFO @ Tue, 30 Jun 2020 02:04:57: Done! pass1 - making usageList (563 chroms): 1 millis pass2 - checking and writing primary data (3935 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:05:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.10_summits.bed INFO @ Tue, 30 Jun 2020 02:05:31: Done! pass1 - making usageList (347 chroms): 1 millis pass2 - checking and writing primary data (857 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:05:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1085379/SRX1085379.20_summits.bed INFO @ Tue, 30 Jun 2020 02:05:59: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 6 millis CompletedMACS2peakCalling