Job ID = 5720915 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,426,294 reads read : 18,852,588 reads written : 9,426,294 reads 0-length : 9,426,294 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: 00:04:18 9426294 reads; of these: 9426294 (100.00%) were unpaired; of these: 307392 (3.26%) aligned 0 times 5877693 (62.35%) aligned exactly 1 time 3241209 (34.38%) aligned >1 times 96.74% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 1082467 / 9118902 = 0.1187 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 03:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.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 03:20:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:20:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:20:31: 1000000 INFO @ Thu, 16 Apr 2020 03:20:37: 2000000 INFO @ Thu, 16 Apr 2020 03:20:43: 3000000 INFO @ Thu, 16 Apr 2020 03:20:48: 4000000 INFO @ Thu, 16 Apr 2020 03:20:53: 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 @ Thu, 16 Apr 2020 03:20:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.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 03:20:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:20:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:20:59: 6000000 INFO @ Thu, 16 Apr 2020 03:21:02: 1000000 INFO @ Thu, 16 Apr 2020 03:21:04: 7000000 INFO @ Thu, 16 Apr 2020 03:21:07: 2000000 INFO @ Thu, 16 Apr 2020 03:21:10: 8000000 INFO @ Thu, 16 Apr 2020 03:21:10: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:21:10: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:21:10: #1 total tags in treatment: 8036435 INFO @ Thu, 16 Apr 2020 03:21:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:21:10: #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 03:21:10: #1 tags after filtering in treatment: 8036435 INFO @ Thu, 16 Apr 2020 03:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:21:10: #1 finished! INFO @ Thu, 16 Apr 2020 03:21:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:21:11: #2 number of paired peaks: 147 WARNING @ Thu, 16 Apr 2020 03:21:11: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 16 Apr 2020 03:21:11: start model_add_line... INFO @ Thu, 16 Apr 2020 03:21:11: start X-correlation... INFO @ Thu, 16 Apr 2020 03:21:11: end of X-cor INFO @ Thu, 16 Apr 2020 03:21:11: #2 finished! INFO @ Thu, 16 Apr 2020 03:21:11: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:21:11: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.05_model.r WARNING @ Thu, 16 Apr 2020 03:21:11: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:21:11: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:21:11: #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 03:21:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:21:13: 3000000 INFO @ Thu, 16 Apr 2020 03:21:19: 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 03:21:24: 5000000 INFO @ Thu, 16 Apr 2020 03:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.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 03:21:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:21:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:21:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:21:30: 6000000 INFO @ Thu, 16 Apr 2020 03:21:32: 1000000 INFO @ Thu, 16 Apr 2020 03:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.05_summits.bed INFO @ Thu, 16 Apr 2020 03:21:35: Done! INFO @ Thu, 16 Apr 2020 03:21:35: 7000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1193 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:21:38: 2000000 INFO @ Thu, 16 Apr 2020 03:21:41: 8000000 INFO @ Thu, 16 Apr 2020 03:21:41: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:21:41: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:21:41: #1 total tags in treatment: 8036435 INFO @ Thu, 16 Apr 2020 03:21:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:21:41: #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 03:21:41: #1 tags after filtering in treatment: 8036435 INFO @ Thu, 16 Apr 2020 03:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:21:41: #1 finished! INFO @ Thu, 16 Apr 2020 03:21:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:21:42: #2 number of paired peaks: 147 WARNING @ Thu, 16 Apr 2020 03:21:42: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 16 Apr 2020 03:21:42: start model_add_line... INFO @ Thu, 16 Apr 2020 03:21:42: start X-correlation... INFO @ Thu, 16 Apr 2020 03:21:42: end of X-cor INFO @ Thu, 16 Apr 2020 03:21:42: #2 finished! INFO @ Thu, 16 Apr 2020 03:21:42: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:21:42: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:21:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.10_model.r WARNING @ Thu, 16 Apr 2020 03:21:42: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:21:42: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:21:42: #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 03:21:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:21:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:21:44: 3000000 INFO @ Thu, 16 Apr 2020 03:21:49: 4000000 INFO @ Thu, 16 Apr 2020 03:21:55: 5000000 INFO @ Thu, 16 Apr 2020 03:21:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:22:00: 6000000 INFO @ Thu, 16 Apr 2020 03:22:06: 7000000 INFO @ Thu, 16 Apr 2020 03:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:22:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:22:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.10_summits.bed INFO @ Thu, 16 Apr 2020 03:22:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (748 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:22:11: 8000000 INFO @ Thu, 16 Apr 2020 03:22:11: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:22:11: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:22:11: #1 total tags in treatment: 8036435 INFO @ Thu, 16 Apr 2020 03:22:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:22:11: #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 03:22:11: #1 tags after filtering in treatment: 8036435 INFO @ Thu, 16 Apr 2020 03:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:22:11: #1 finished! INFO @ Thu, 16 Apr 2020 03:22:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:22:12: #2 number of paired peaks: 147 WARNING @ Thu, 16 Apr 2020 03:22:12: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 16 Apr 2020 03:22:12: start model_add_line... INFO @ Thu, 16 Apr 2020 03:22:12: start X-correlation... INFO @ Thu, 16 Apr 2020 03:22:12: end of X-cor INFO @ Thu, 16 Apr 2020 03:22:12: #2 finished! INFO @ Thu, 16 Apr 2020 03:22:12: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:22:12: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.20_model.r WARNING @ Thu, 16 Apr 2020 03:22:12: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:22:12: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:22:12: #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 03:22:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:22:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775942/SRX5775942.20_summits.bed INFO @ Thu, 16 Apr 2020 03:22:37: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (328 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。