Job ID = 5720700 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,681,967 reads read : 18,681,967 reads written : 18,681,967 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: 00:06:13 18681967 reads; of these: 18681967 (100.00%) were unpaired; of these: 426255 (2.28%) aligned 0 times 11350205 (60.75%) aligned exactly 1 time 6905507 (36.96%) aligned >1 times 97.72% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 1948238 / 18255712 = 0.1067 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 01:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.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 01:19:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:28: 1000000 INFO @ Thu, 16 Apr 2020 01:19:33: 2000000 INFO @ Thu, 16 Apr 2020 01:19:37: 3000000 INFO @ Thu, 16 Apr 2020 01:19:42: 4000000 INFO @ Thu, 16 Apr 2020 01:19:47: 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 01:19:51: 6000000 INFO @ Thu, 16 Apr 2020 01:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.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 01:19:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:56: 7000000 INFO @ Thu, 16 Apr 2020 01:19:57: 1000000 INFO @ Thu, 16 Apr 2020 01:20:01: 8000000 INFO @ Thu, 16 Apr 2020 01:20:02: 2000000 INFO @ Thu, 16 Apr 2020 01:20:06: 9000000 INFO @ Thu, 16 Apr 2020 01:20:07: 3000000 INFO @ Thu, 16 Apr 2020 01:20:10: 10000000 INFO @ Thu, 16 Apr 2020 01:20:11: 4000000 INFO @ Thu, 16 Apr 2020 01:20:15: 11000000 INFO @ Thu, 16 Apr 2020 01:20:16: 5000000 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 01:20:20: 12000000 INFO @ Thu, 16 Apr 2020 01:20:21: 6000000 INFO @ Thu, 16 Apr 2020 01:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.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 01:20:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:24: 13000000 INFO @ Thu, 16 Apr 2020 01:20:26: 7000000 INFO @ Thu, 16 Apr 2020 01:20:28: 1000000 INFO @ Thu, 16 Apr 2020 01:20:29: 14000000 INFO @ Thu, 16 Apr 2020 01:20:30: 8000000 INFO @ Thu, 16 Apr 2020 01:20:34: 2000000 INFO @ Thu, 16 Apr 2020 01:20:34: 15000000 INFO @ Thu, 16 Apr 2020 01:20:35: 9000000 INFO @ Thu, 16 Apr 2020 01:20:39: 16000000 INFO @ Thu, 16 Apr 2020 01:20:39: 3000000 INFO @ Thu, 16 Apr 2020 01:20:40: 10000000 INFO @ Thu, 16 Apr 2020 01:20:40: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:20:40: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:20:40: #1 total tags in treatment: 16307474 INFO @ Thu, 16 Apr 2020 01:20:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:40: #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 01:20:41: #1 tags after filtering in treatment: 16307474 INFO @ Thu, 16 Apr 2020 01:20:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:41: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:42: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 01:20:42: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 01:20:42: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:42: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:42: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:42: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:42: #2 predicted fragment length is 33 bps INFO @ Thu, 16 Apr 2020 01:20:42: #2 alternative fragment length(s) may be 2,33,40 bps INFO @ Thu, 16 Apr 2020 01:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.05_model.r WARNING @ Thu, 16 Apr 2020 01:20:42: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:20:42: #2 You may need to consider one of the other alternative d(s): 2,33,40 WARNING @ Thu, 16 Apr 2020 01:20:42: #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 01:20:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:45: 11000000 INFO @ Thu, 16 Apr 2020 01:20:45: 4000000 INFO @ Thu, 16 Apr 2020 01:20:49: 12000000 INFO @ Thu, 16 Apr 2020 01:20:50: 5000000 INFO @ Thu, 16 Apr 2020 01:20:54: 13000000 INFO @ Thu, 16 Apr 2020 01:20:55: 6000000 INFO @ Thu, 16 Apr 2020 01:20:59: 14000000 INFO @ Thu, 16 Apr 2020 01:21:01: 7000000 INFO @ Thu, 16 Apr 2020 01:21:04: 15000000 INFO @ Thu, 16 Apr 2020 01:21:06: 8000000 INFO @ Thu, 16 Apr 2020 01:21:08: 16000000 INFO @ Thu, 16 Apr 2020 01:21:10: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:21:10: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:21:10: #1 total tags in treatment: 16307474 INFO @ Thu, 16 Apr 2020 01:21:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:10: #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 01:21:10: #1 tags after filtering in treatment: 16307474 INFO @ Thu, 16 Apr 2020 01:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:10: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:11: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 01:21:11: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:11: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:11: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:11: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:11: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:11: #2 predicted fragment length is 33 bps INFO @ Thu, 16 Apr 2020 01:21:11: #2 alternative fragment length(s) may be 2,33,40 bps INFO @ Thu, 16 Apr 2020 01:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.10_model.r WARNING @ Thu, 16 Apr 2020 01:21:11: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:11: #2 You may need to consider one of the other alternative d(s): 2,33,40 WARNING @ Thu, 16 Apr 2020 01:21:11: #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 01:21:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:11: 9000000 INFO @ Thu, 16 Apr 2020 01:21:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:16: 10000000 INFO @ Thu, 16 Apr 2020 01:21:22: 11000000 INFO @ Thu, 16 Apr 2020 01:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.05_summits.bed INFO @ Thu, 16 Apr 2020 01:21:26: Done! INFO @ Thu, 16 Apr 2020 01:21:27: 12000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2686 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:21:32: 13000000 INFO @ Thu, 16 Apr 2020 01:21:37: 14000000 INFO @ Thu, 16 Apr 2020 01:21:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:42: 15000000 INFO @ Thu, 16 Apr 2020 01:21:48: 16000000 INFO @ Thu, 16 Apr 2020 01:21:49: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:21:49: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:21:49: #1 total tags in treatment: 16307474 INFO @ Thu, 16 Apr 2020 01:21:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:49: #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 01:21:49: #1 tags after filtering in treatment: 16307474 INFO @ Thu, 16 Apr 2020 01:21:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:49: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:51: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 01:21:51: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:51: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:51: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:51: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:51: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:51: #2 predicted fragment length is 33 bps INFO @ Thu, 16 Apr 2020 01:21:51: #2 alternative fragment length(s) may be 2,33,40 bps INFO @ Thu, 16 Apr 2020 01:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.20_model.r WARNING @ Thu, 16 Apr 2020 01:21:51: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:51: #2 You may need to consider one of the other alternative d(s): 2,33,40 WARNING @ Thu, 16 Apr 2020 01:21:51: #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 01:21:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.10_summits.bed INFO @ Thu, 16 Apr 2020 01:21:57: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1200 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:22:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158164/SRX4158164.20_summits.bed INFO @ Thu, 16 Apr 2020 01:22:35: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (413 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。