Job ID = 5720724 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,555,159 reads read : 9,555,159 reads written : 9,555,159 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:03:40 9555159 reads; of these: 9555159 (100.00%) were unpaired; of these: 616352 (6.45%) aligned 0 times 4619160 (48.34%) aligned exactly 1 time 4319647 (45.21%) aligned >1 times 93.55% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1615106 / 8938807 = 0.1807 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 @ Thu, 16 Apr 2020 01:10:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.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 @ Thu, 16 Apr 2020 01:10:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:47: 1000000 INFO @ Thu, 16 Apr 2020 01:10:53: 2000000 INFO @ Thu, 16 Apr 2020 01:10:59: 3000000 INFO @ Thu, 16 Apr 2020 01:11:04: 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 @ Thu, 16 Apr 2020 01:11:10: 5000000 INFO @ Thu, 16 Apr 2020 01:11:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.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 @ Thu, 16 Apr 2020 01:11:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:11:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:11:16: 6000000 INFO @ Thu, 16 Apr 2020 01:11:18: 1000000 INFO @ Thu, 16 Apr 2020 01:11:23: 7000000 INFO @ Thu, 16 Apr 2020 01:11:24: 2000000 INFO @ Thu, 16 Apr 2020 01:11:25: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:11:25: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:11:25: #1 total tags in treatment: 7323701 INFO @ Thu, 16 Apr 2020 01:11:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:11:25: #1 tags after filtering in treatment: 7323701 INFO @ Thu, 16 Apr 2020 01:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:25: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:25: #2 number of paired peaks: 975 WARNING @ Thu, 16 Apr 2020 01:11:25: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Thu, 16 Apr 2020 01:11:25: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:25: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:25: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:25: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:25: #2 predicted fragment length is 63 bps INFO @ Thu, 16 Apr 2020 01:11:25: #2 alternative fragment length(s) may be 63 bps INFO @ Thu, 16 Apr 2020 01:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.05_model.r WARNING @ Thu, 16 Apr 2020 01:11:25: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:11:25: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Thu, 16 Apr 2020 01:11:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:11:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:11:30: 3000000 INFO @ Thu, 16 Apr 2020 01:11:37: 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 @ Thu, 16 Apr 2020 01:11:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:11:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.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 @ Thu, 16 Apr 2020 01:11:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:11:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:11:43: 5000000 INFO @ Thu, 16 Apr 2020 01:11:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.05_summits.bed INFO @ Thu, 16 Apr 2020 01:11:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4568 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:11:48: 1000000 INFO @ Thu, 16 Apr 2020 01:11:50: 6000000 INFO @ Thu, 16 Apr 2020 01:11:55: 2000000 INFO @ Thu, 16 Apr 2020 01:11:56: 7000000 INFO @ Thu, 16 Apr 2020 01:11:58: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:11:58: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:11:58: #1 total tags in treatment: 7323701 INFO @ Thu, 16 Apr 2020 01:11:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:11:59: #1 tags after filtering in treatment: 7323701 INFO @ Thu, 16 Apr 2020 01:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:59: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:59: #2 number of paired peaks: 975 WARNING @ Thu, 16 Apr 2020 01:11:59: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Thu, 16 Apr 2020 01:11:59: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:59: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:59: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:59: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:59: #2 predicted fragment length is 63 bps INFO @ Thu, 16 Apr 2020 01:11:59: #2 alternative fragment length(s) may be 63 bps INFO @ Thu, 16 Apr 2020 01:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.10_model.r WARNING @ Thu, 16 Apr 2020 01:11:59: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:11:59: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Thu, 16 Apr 2020 01:11:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:11:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:12:02: 3000000 INFO @ Thu, 16 Apr 2020 01:12:08: 4000000 INFO @ Thu, 16 Apr 2020 01:12:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:14: 5000000 INFO @ Thu, 16 Apr 2020 01:12:21: 6000000 INFO @ Thu, 16 Apr 2020 01:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.10_summits.bed INFO @ Thu, 16 Apr 2020 01:12:22: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1781 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:12:27: 7000000 INFO @ Thu, 16 Apr 2020 01:12:29: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:12:29: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:12:29: #1 total tags in treatment: 7323701 INFO @ Thu, 16 Apr 2020 01:12:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:12:29: #1 tags after filtering in treatment: 7323701 INFO @ Thu, 16 Apr 2020 01:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:12:29: #1 finished! INFO @ Thu, 16 Apr 2020 01:12:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:12:30: #2 number of paired peaks: 975 WARNING @ Thu, 16 Apr 2020 01:12:30: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Thu, 16 Apr 2020 01:12:30: start model_add_line... INFO @ Thu, 16 Apr 2020 01:12:30: start X-correlation... INFO @ Thu, 16 Apr 2020 01:12:30: end of X-cor INFO @ Thu, 16 Apr 2020 01:12:30: #2 finished! INFO @ Thu, 16 Apr 2020 01:12:30: #2 predicted fragment length is 63 bps INFO @ Thu, 16 Apr 2020 01:12:30: #2 alternative fragment length(s) may be 63 bps INFO @ Thu, 16 Apr 2020 01:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.20_model.r WARNING @ Thu, 16 Apr 2020 01:12:30: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:12:30: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Thu, 16 Apr 2020 01:12:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:12:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:12:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158196/SRX4158196.20_summits.bed INFO @ Thu, 16 Apr 2020 01:12:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (988 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。