Job ID = 5721298 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,497,360 reads read : 20,497,360 reads written : 20,497,360 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: 00:06:25 20497360 reads; of these: 20497360 (100.00%) were unpaired; of these: 2546206 (12.42%) aligned 0 times 12722097 (62.07%) aligned exactly 1 time 5229057 (25.51%) aligned >1 times 87.58% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1648595 / 17951154 = 0.0918 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 06:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.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 06:37:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:37:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:37:18: 1000000 INFO @ Thu, 16 Apr 2020 06:37:22: 2000000 INFO @ Thu, 16 Apr 2020 06:37:27: 3000000 INFO @ Thu, 16 Apr 2020 06:37:32: 4000000 INFO @ Thu, 16 Apr 2020 06:37:36: 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 06:37:41: 6000000 INFO @ Thu, 16 Apr 2020 06:37:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.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 06:37:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:37:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:37:46: 7000000 INFO @ Thu, 16 Apr 2020 06:37:48: 1000000 INFO @ Thu, 16 Apr 2020 06:37:51: 8000000 INFO @ Thu, 16 Apr 2020 06:37:54: 2000000 INFO @ Thu, 16 Apr 2020 06:37:56: 9000000 INFO @ Thu, 16 Apr 2020 06:37:59: 3000000 INFO @ Thu, 16 Apr 2020 06:38:01: 10000000 INFO @ Thu, 16 Apr 2020 06:38:05: 4000000 INFO @ Thu, 16 Apr 2020 06:38:06: 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 @ Thu, 16 Apr 2020 06:38:10: 5000000 INFO @ Thu, 16 Apr 2020 06:38:10: 12000000 INFO @ Thu, 16 Apr 2020 06:38:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.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 06:38:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:38:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:38:15: 13000000 INFO @ Thu, 16 Apr 2020 06:38:16: 6000000 INFO @ Thu, 16 Apr 2020 06:38:18: 1000000 INFO @ Thu, 16 Apr 2020 06:38:20: 14000000 INFO @ Thu, 16 Apr 2020 06:38:21: 7000000 INFO @ Thu, 16 Apr 2020 06:38:24: 2000000 INFO @ Thu, 16 Apr 2020 06:38:25: 15000000 INFO @ Thu, 16 Apr 2020 06:38:28: 8000000 INFO @ Thu, 16 Apr 2020 06:38:29: 3000000 INFO @ Thu, 16 Apr 2020 06:38:30: 16000000 INFO @ Thu, 16 Apr 2020 06:38:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:38:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:38:32: #1 total tags in treatment: 16302559 INFO @ Thu, 16 Apr 2020 06:38:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:38:32: #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 06:38:32: #1 tags after filtering in treatment: 16302559 INFO @ Thu, 16 Apr 2020 06:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:38:32: #1 finished! INFO @ Thu, 16 Apr 2020 06:38:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:38:33: #2 number of paired peaks: 101 WARNING @ Thu, 16 Apr 2020 06:38:33: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Thu, 16 Apr 2020 06:38:33: start model_add_line... INFO @ Thu, 16 Apr 2020 06:38:33: start X-correlation... INFO @ Thu, 16 Apr 2020 06:38:33: end of X-cor INFO @ Thu, 16 Apr 2020 06:38:33: #2 finished! INFO @ Thu, 16 Apr 2020 06:38:33: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:38:33: #2 alternative fragment length(s) may be 4,48 bps INFO @ Thu, 16 Apr 2020 06:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.05_model.r WARNING @ Thu, 16 Apr 2020 06:38:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:38:33: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Thu, 16 Apr 2020 06:38:33: #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 06:38:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:38:35: 4000000 INFO @ Thu, 16 Apr 2020 06:38:35: 9000000 INFO @ Thu, 16 Apr 2020 06:38:40: 5000000 INFO @ Thu, 16 Apr 2020 06:38:42: 10000000 INFO @ Thu, 16 Apr 2020 06:38:46: 6000000 INFO @ Thu, 16 Apr 2020 06:38:49: 11000000 INFO @ Thu, 16 Apr 2020 06:38:52: 7000000 INFO @ Thu, 16 Apr 2020 06:38:56: 12000000 INFO @ Thu, 16 Apr 2020 06:38:57: 8000000 INFO @ Thu, 16 Apr 2020 06:39:02: 13000000 INFO @ Thu, 16 Apr 2020 06:39:03: 9000000 INFO @ Thu, 16 Apr 2020 06:39:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:39:08: 14000000 INFO @ Thu, 16 Apr 2020 06:39:08: 10000000 INFO @ Thu, 16 Apr 2020 06:39:13: 15000000 INFO @ Thu, 16 Apr 2020 06:39:14: 11000000 INFO @ Thu, 16 Apr 2020 06:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.05_summits.bed INFO @ Thu, 16 Apr 2020 06:39:18: Done! INFO @ Thu, 16 Apr 2020 06:39:19: 16000000 INFO @ Thu, 16 Apr 2020 06:39:19: 12000000 INFO @ Thu, 16 Apr 2020 06:39:21: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:39:21: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:39:21: #1 total tags in treatment: 16302559 INFO @ Thu, 16 Apr 2020 06:39:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:39:21: #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 06:39:21: #1 tags after filtering in treatment: 16302559 INFO @ Thu, 16 Apr 2020 06:39:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:39:21: #1 finished! INFO @ Thu, 16 Apr 2020 06:39:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:39:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:39:22: #2 number of paired peaks: 101 WARNING @ Thu, 16 Apr 2020 06:39:22: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Thu, 16 Apr 2020 06:39:22: start model_add_line... INFO @ Thu, 16 Apr 2020 06:39:22: start X-correlation... INFO @ Thu, 16 Apr 2020 06:39:22: end of X-cor INFO @ Thu, 16 Apr 2020 06:39:22: #2 finished! INFO @ Thu, 16 Apr 2020 06:39:22: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:39:22: #2 alternative fragment length(s) may be 4,48 bps INFO @ Thu, 16 Apr 2020 06:39:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.10_model.r WARNING @ Thu, 16 Apr 2020 06:39:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:39:22: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Thu, 16 Apr 2020 06:39:22: #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 06:39:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:39:22: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1723 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:39:25: 13000000 INFO @ Thu, 16 Apr 2020 06:39:30: 14000000 INFO @ Thu, 16 Apr 2020 06:39:36: 15000000 INFO @ Thu, 16 Apr 2020 06:39:41: 16000000 INFO @ Thu, 16 Apr 2020 06:39:43: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:39:43: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:39:43: #1 total tags in treatment: 16302559 INFO @ Thu, 16 Apr 2020 06:39:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:39:43: #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 06:39:43: #1 tags after filtering in treatment: 16302559 INFO @ Thu, 16 Apr 2020 06:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:39:43: #1 finished! INFO @ Thu, 16 Apr 2020 06:39:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:39:44: #2 number of paired peaks: 101 WARNING @ Thu, 16 Apr 2020 06:39:44: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Thu, 16 Apr 2020 06:39:44: start model_add_line... INFO @ Thu, 16 Apr 2020 06:39:44: start X-correlation... INFO @ Thu, 16 Apr 2020 06:39:44: end of X-cor INFO @ Thu, 16 Apr 2020 06:39:44: #2 finished! INFO @ Thu, 16 Apr 2020 06:39:44: #2 predicted fragment length is 48 bps INFO @ Thu, 16 Apr 2020 06:39:44: #2 alternative fragment length(s) may be 4,48 bps INFO @ Thu, 16 Apr 2020 06:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.20_model.r WARNING @ Thu, 16 Apr 2020 06:39:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:39:44: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Thu, 16 Apr 2020 06:39:44: #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 06:39:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:39:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:40:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:40:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:40:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.10_summits.bed INFO @ Thu, 16 Apr 2020 06:40:06: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1302 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:40:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7672890/SRX7672890.20_summits.bed INFO @ Thu, 16 Apr 2020 06:40:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (755 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。