Job ID = 5720751 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,671,478 reads read : 41,342,956 reads written : 20,671,478 reads 0-length : 20,671,478 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: 00:08:22 20671478 reads; of these: 20671478 (100.00%) were unpaired; of these: 965334 (4.67%) aligned 0 times 14581068 (70.54%) aligned exactly 1 time 5125076 (24.79%) aligned >1 times 95.33% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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 12 files... [bam_rmdupse_core] 2057412 / 19706144 = 0.1044 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 01:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.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 01:32:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:11: 1000000 INFO @ Thu, 16 Apr 2020 01:32:17: 2000000 INFO @ Thu, 16 Apr 2020 01:32:24: 3000000 INFO @ Thu, 16 Apr 2020 01:32:30: 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 01:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.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 01:32:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:36: 5000000 INFO @ Thu, 16 Apr 2020 01:32:41: 1000000 INFO @ Thu, 16 Apr 2020 01:32:43: 6000000 INFO @ Thu, 16 Apr 2020 01:32:48: 2000000 INFO @ Thu, 16 Apr 2020 01:32:49: 7000000 INFO @ Thu, 16 Apr 2020 01:32:54: 3000000 INFO @ Thu, 16 Apr 2020 01:32:56: 8000000 INFO @ Thu, 16 Apr 2020 01:33:01: 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 01:33:02: 9000000 INFO @ Thu, 16 Apr 2020 01:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.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 01:33:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:33:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:33:07: 5000000 INFO @ Thu, 16 Apr 2020 01:33:08: 10000000 INFO @ Thu, 16 Apr 2020 01:33:12: 1000000 INFO @ Thu, 16 Apr 2020 01:33:13: 6000000 INFO @ Thu, 16 Apr 2020 01:33:15: 11000000 INFO @ Thu, 16 Apr 2020 01:33:19: 2000000 INFO @ Thu, 16 Apr 2020 01:33:20: 7000000 INFO @ Thu, 16 Apr 2020 01:33:21: 12000000 INFO @ Thu, 16 Apr 2020 01:33:25: 3000000 INFO @ Thu, 16 Apr 2020 01:33:26: 8000000 INFO @ Thu, 16 Apr 2020 01:33:28: 13000000 INFO @ Thu, 16 Apr 2020 01:33:32: 4000000 INFO @ Thu, 16 Apr 2020 01:33:33: 9000000 INFO @ Thu, 16 Apr 2020 01:33:34: 14000000 INFO @ Thu, 16 Apr 2020 01:33:38: 5000000 INFO @ Thu, 16 Apr 2020 01:33:39: 10000000 INFO @ Thu, 16 Apr 2020 01:33:41: 15000000 INFO @ Thu, 16 Apr 2020 01:33:44: 6000000 INFO @ Thu, 16 Apr 2020 01:33:46: 11000000 INFO @ Thu, 16 Apr 2020 01:33:47: 16000000 INFO @ Thu, 16 Apr 2020 01:33:51: 7000000 INFO @ Thu, 16 Apr 2020 01:33:52: 12000000 INFO @ Thu, 16 Apr 2020 01:33:54: 17000000 INFO @ Thu, 16 Apr 2020 01:33:58: 8000000 INFO @ Thu, 16 Apr 2020 01:33:58: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:33:58: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:33:58: #1 total tags in treatment: 17648732 INFO @ Thu, 16 Apr 2020 01:33:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:33:58: #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 01:33:58: #1 tags after filtering in treatment: 17648732 INFO @ Thu, 16 Apr 2020 01:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:33:58: #1 finished! INFO @ Thu, 16 Apr 2020 01:33:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:33:58: 13000000 INFO @ Thu, 16 Apr 2020 01:33:59: #2 number of paired peaks: 536 WARNING @ Thu, 16 Apr 2020 01:33:59: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 16 Apr 2020 01:33:59: start model_add_line... INFO @ Thu, 16 Apr 2020 01:34:00: start X-correlation... INFO @ Thu, 16 Apr 2020 01:34:00: end of X-cor INFO @ Thu, 16 Apr 2020 01:34:00: #2 finished! INFO @ Thu, 16 Apr 2020 01:34:00: #2 predicted fragment length is 77 bps INFO @ Thu, 16 Apr 2020 01:34:00: #2 alternative fragment length(s) may be 4,77 bps INFO @ Thu, 16 Apr 2020 01:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.05_model.r WARNING @ Thu, 16 Apr 2020 01:34:00: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:34:00: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Thu, 16 Apr 2020 01:34:00: #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 01:34:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:34:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:34:04: 9000000 INFO @ Thu, 16 Apr 2020 01:34:05: 14000000 INFO @ Thu, 16 Apr 2020 01:34:10: 10000000 INFO @ Thu, 16 Apr 2020 01:34:11: 15000000 INFO @ Thu, 16 Apr 2020 01:34:17: 11000000 INFO @ Thu, 16 Apr 2020 01:34:18: 16000000 INFO @ Thu, 16 Apr 2020 01:34:23: 12000000 INFO @ Thu, 16 Apr 2020 01:34:24: 17000000 INFO @ Thu, 16 Apr 2020 01:34:28: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:34:28: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:34:28: #1 total tags in treatment: 17648732 INFO @ Thu, 16 Apr 2020 01:34:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:34:28: #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 01:34:28: #1 tags after filtering in treatment: 17648732 INFO @ Thu, 16 Apr 2020 01:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:34:28: #1 finished! INFO @ Thu, 16 Apr 2020 01:34:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:34:29: 13000000 INFO @ Thu, 16 Apr 2020 01:34:30: #2 number of paired peaks: 536 WARNING @ Thu, 16 Apr 2020 01:34:30: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 16 Apr 2020 01:34:30: start model_add_line... INFO @ Thu, 16 Apr 2020 01:34:30: start X-correlation... INFO @ Thu, 16 Apr 2020 01:34:30: end of X-cor INFO @ Thu, 16 Apr 2020 01:34:30: #2 finished! INFO @ Thu, 16 Apr 2020 01:34:30: #2 predicted fragment length is 77 bps INFO @ Thu, 16 Apr 2020 01:34:30: #2 alternative fragment length(s) may be 4,77 bps INFO @ Thu, 16 Apr 2020 01:34:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.10_model.r WARNING @ Thu, 16 Apr 2020 01:34:30: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:34:30: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Thu, 16 Apr 2020 01:34:30: #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 01:34:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:34:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:34:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:34:35: 14000000 INFO @ Thu, 16 Apr 2020 01:34:42: 15000000 INFO @ Thu, 16 Apr 2020 01:34:48: 16000000 INFO @ Thu, 16 Apr 2020 01:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.05_summits.bed INFO @ Thu, 16 Apr 2020 01:34:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5672 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:34:54: 17000000 INFO @ Thu, 16 Apr 2020 01:34:58: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:34:58: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:34:58: #1 total tags in treatment: 17648732 INFO @ Thu, 16 Apr 2020 01:34:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:34:58: #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 01:34:58: #1 tags after filtering in treatment: 17648732 INFO @ Thu, 16 Apr 2020 01:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:34:58: #1 finished! INFO @ Thu, 16 Apr 2020 01:34:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:34:59: #2 number of paired peaks: 536 WARNING @ Thu, 16 Apr 2020 01:34:59: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 16 Apr 2020 01:34:59: start model_add_line... INFO @ Thu, 16 Apr 2020 01:35:00: start X-correlation... INFO @ Thu, 16 Apr 2020 01:35:00: end of X-cor INFO @ Thu, 16 Apr 2020 01:35:00: #2 finished! INFO @ Thu, 16 Apr 2020 01:35:00: #2 predicted fragment length is 77 bps INFO @ Thu, 16 Apr 2020 01:35:00: #2 alternative fragment length(s) may be 4,77 bps INFO @ Thu, 16 Apr 2020 01:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.20_model.r WARNING @ Thu, 16 Apr 2020 01:35:00: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:35:00: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Thu, 16 Apr 2020 01:35:00: #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 01:35:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:35:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.10_summits.bed INFO @ Thu, 16 Apr 2020 01:35:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2491 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:35:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226989/SRX5226989.20_summits.bed INFO @ Thu, 16 Apr 2020 01:35:48: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (940 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。