Job ID = 6529418 SRX = SRX2592426 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: 00:00:01 Multiseed full-index search: 00:08:40 24443080 reads; of these: 24443080 (100.00%) were unpaired; of these: 1946198 (7.96%) aligned 0 times 16286425 (66.63%) aligned exactly 1 time 6210457 (25.41%) aligned >1 times 92.04% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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 12 files... [bam_rmdupse_core] 5612377 / 22496882 = 0.2495 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 02:03:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.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 02:03:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:03:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:03:21: 1000000 INFO @ Tue, 30 Jun 2020 02:03:26: 2000000 INFO @ Tue, 30 Jun 2020 02:03:31: 3000000 INFO @ Tue, 30 Jun 2020 02:03:36: 4000000 INFO @ Tue, 30 Jun 2020 02:03:40: 5000000 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 02:03:46: 6000000 INFO @ Tue, 30 Jun 2020 02:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.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 02:03:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:03:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:03:50: 7000000 INFO @ Tue, 30 Jun 2020 02:03:52: 1000000 INFO @ Tue, 30 Jun 2020 02:03:55: 8000000 INFO @ Tue, 30 Jun 2020 02:03:57: 2000000 INFO @ Tue, 30 Jun 2020 02:04:01: 9000000 INFO @ Tue, 30 Jun 2020 02:04:03: 3000000 INFO @ Tue, 30 Jun 2020 02:04:06: 10000000 INFO @ Tue, 30 Jun 2020 02:04:09: 4000000 INFO @ Tue, 30 Jun 2020 02:04:11: 11000000 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 02:04:14: 5000000 INFO @ Tue, 30 Jun 2020 02:04:16: 12000000 INFO @ Tue, 30 Jun 2020 02:04:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.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 02:04:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:20: 6000000 INFO @ Tue, 30 Jun 2020 02:04:21: 13000000 INFO @ Tue, 30 Jun 2020 02:04:21: 1000000 INFO @ Tue, 30 Jun 2020 02:04:25: 7000000 INFO @ Tue, 30 Jun 2020 02:04:26: 14000000 INFO @ Tue, 30 Jun 2020 02:04:27: 2000000 INFO @ Tue, 30 Jun 2020 02:04:31: 8000000 INFO @ Tue, 30 Jun 2020 02:04:31: 15000000 INFO @ Tue, 30 Jun 2020 02:04:32: 3000000 INFO @ Tue, 30 Jun 2020 02:04:37: 16000000 INFO @ Tue, 30 Jun 2020 02:04:37: 4000000 INFO @ Tue, 30 Jun 2020 02:04:37: 9000000 INFO @ Tue, 30 Jun 2020 02:04:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:04:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:04:41: #1 total tags in treatment: 16884505 INFO @ Tue, 30 Jun 2020 02:04:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:04:41: #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 02:04:42: 5000000 INFO @ Tue, 30 Jun 2020 02:04:42: #1 tags after filtering in treatment: 16884447 INFO @ Tue, 30 Jun 2020 02:04:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:04:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:04:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:04:43: 10000000 INFO @ Tue, 30 Jun 2020 02:04:43: #2 number of paired peaks: 262 WARNING @ Tue, 30 Jun 2020 02:04:43: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 30 Jun 2020 02:04:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:04:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:04:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:04:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:04:43: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:04:43: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:04:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.05_model.r WARNING @ Tue, 30 Jun 2020 02:04:43: #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 02:04:43: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:04:43: #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 02:04:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:04:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:04:47: 6000000 INFO @ Tue, 30 Jun 2020 02:04:48: 11000000 INFO @ Tue, 30 Jun 2020 02:04:52: 7000000 INFO @ Tue, 30 Jun 2020 02:04:54: 12000000 INFO @ Tue, 30 Jun 2020 02:04:57: 8000000 INFO @ Tue, 30 Jun 2020 02:05:00: 13000000 INFO @ Tue, 30 Jun 2020 02:05:03: 9000000 INFO @ Tue, 30 Jun 2020 02:05:06: 14000000 INFO @ Tue, 30 Jun 2020 02:05:08: 10000000 INFO @ Tue, 30 Jun 2020 02:05:12: 15000000 INFO @ Tue, 30 Jun 2020 02:05:13: 11000000 INFO @ Tue, 30 Jun 2020 02:05:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:17: 16000000 INFO @ Tue, 30 Jun 2020 02:05:18: 12000000 INFO @ Tue, 30 Jun 2020 02:05:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:05:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:05:23: #1 total tags in treatment: 16884505 INFO @ Tue, 30 Jun 2020 02:05:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:23: #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 02:05:23: 13000000 INFO @ Tue, 30 Jun 2020 02:05:23: #1 tags after filtering in treatment: 16884447 INFO @ Tue, 30 Jun 2020 02:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:25: #2 number of paired peaks: 262 WARNING @ Tue, 30 Jun 2020 02:05:25: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:25: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:05:25: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:05:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.10_model.r WARNING @ Tue, 30 Jun 2020 02:05:25: #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 02:05:25: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:05:25: #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 02:05:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:28: 14000000 INFO @ Tue, 30 Jun 2020 02:05:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:05:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:05:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.05_summits.bed INFO @ Tue, 30 Jun 2020 02:05:29: Done! pass1 - making usageList (754 chroms): 2 millis pass2 - checking and writing primary data (13148 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:05:33: 15000000 INFO @ Tue, 30 Jun 2020 02:05:38: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:05:43: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:05:43: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:05:43: #1 total tags in treatment: 16884505 INFO @ Tue, 30 Jun 2020 02:05:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:43: #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 02:05:44: #1 tags after filtering in treatment: 16884447 INFO @ Tue, 30 Jun 2020 02:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:45: #2 number of paired peaks: 262 WARNING @ Tue, 30 Jun 2020 02:05:45: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:45: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:05:45: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:05:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.20_model.r WARNING @ Tue, 30 Jun 2020 02:05:45: #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 02:05:45: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:05:45: #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 02:05:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.10_summits.bed INFO @ Tue, 30 Jun 2020 02:06:11: Done! pass1 - making usageList (531 chroms): 2 millis pass2 - checking and writing primary data (6932 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:06:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:06:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592426/SRX2592426.20_summits.bed INFO @ Tue, 30 Jun 2020 02:06:30: Done! pass1 - making usageList (239 chroms): 1 millis pass2 - checking and writing primary data (874 records, 4 fields): 8 millis CompletedMACS2peakCalling