Job ID = 5720955 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,091,201 reads read : 9,091,201 reads written : 9,091,201 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: 00:04:24 9091201 reads; of these: 9091201 (100.00%) were unpaired; of these: 401313 (4.41%) aligned 0 times 5296932 (58.26%) aligned exactly 1 time 3392956 (37.32%) aligned >1 times 95.59% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 3098808 / 8689888 = 0.3566 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 03:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.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 03:37:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:37:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:37:25: 1000000 INFO @ Thu, 16 Apr 2020 03:37:30: 2000000 INFO @ Thu, 16 Apr 2020 03:37:35: 3000000 INFO @ Thu, 16 Apr 2020 03:37:40: 4000000 INFO @ Thu, 16 Apr 2020 03:37:44: 5000000 INFO @ Thu, 16 Apr 2020 03:37:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:37:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:37:47: #1 total tags in treatment: 5591080 INFO @ Thu, 16 Apr 2020 03:37:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:37:47: #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 03:37:47: #1 tags after filtering in treatment: 5591080 INFO @ Thu, 16 Apr 2020 03:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:37:47: #1 finished! INFO @ Thu, 16 Apr 2020 03:37:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:37:48: #2 number of paired peaks: 1289 INFO @ Thu, 16 Apr 2020 03:37:48: start model_add_line... INFO @ Thu, 16 Apr 2020 03:37:48: start X-correlation... INFO @ Thu, 16 Apr 2020 03:37:48: end of X-cor INFO @ Thu, 16 Apr 2020 03:37:48: #2 finished! INFO @ Thu, 16 Apr 2020 03:37:48: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 03:37:48: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 03:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.05_model.r WARNING @ Thu, 16 Apr 2020 03:37:48: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:37:48: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 03:37:48: #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 03:37:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:37:48: #3 Pre-compute pvalue-qvalue table... 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 03:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.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 03:37:50: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:37:50: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:37:55: 1000000 INFO @ Thu, 16 Apr 2020 03:37:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:38:00: 2000000 INFO @ Thu, 16 Apr 2020 03:38:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:38:05: 3000000 INFO @ Thu, 16 Apr 2020 03:38:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:38:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.05_summits.bed INFO @ Thu, 16 Apr 2020 03:38:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7469 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:38:10: 4000000 INFO @ Thu, 16 Apr 2020 03:38:14: 5000000 INFO @ Thu, 16 Apr 2020 03:38:17: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:38:17: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:38:17: #1 total tags in treatment: 5591080 INFO @ Thu, 16 Apr 2020 03:38:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:38:17: #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 03:38:17: #1 tags after filtering in treatment: 5591080 INFO @ Thu, 16 Apr 2020 03:38:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:38:17: #1 finished! INFO @ Thu, 16 Apr 2020 03:38:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:38:18: #2 number of paired peaks: 1289 INFO @ Thu, 16 Apr 2020 03:38:18: start model_add_line... INFO @ Thu, 16 Apr 2020 03:38:18: start X-correlation... INFO @ Thu, 16 Apr 2020 03:38:18: end of X-cor INFO @ Thu, 16 Apr 2020 03:38:18: #2 finished! INFO @ Thu, 16 Apr 2020 03:38:18: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 03:38:18: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 03:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.10_model.r WARNING @ Thu, 16 Apr 2020 03:38:18: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:38:18: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 03:38:18: #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 03:38:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:38:18: #3 Pre-compute pvalue-qvalue table... 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 03:38:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.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 03:38:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:38:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:38:25: 1000000 INFO @ Thu, 16 Apr 2020 03:38:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:38:30: 2000000 INFO @ Thu, 16 Apr 2020 03:38:35: 3000000 INFO @ Thu, 16 Apr 2020 03:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:38:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.10_summits.bed INFO @ Thu, 16 Apr 2020 03:38:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1875 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:38:39: 4000000 INFO @ Thu, 16 Apr 2020 03:38:44: 5000000 INFO @ Thu, 16 Apr 2020 03:38:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:38:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:38:47: #1 total tags in treatment: 5591080 INFO @ Thu, 16 Apr 2020 03:38:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:38:47: #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 03:38:47: #1 tags after filtering in treatment: 5591080 INFO @ Thu, 16 Apr 2020 03:38:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:38:47: #1 finished! INFO @ Thu, 16 Apr 2020 03:38:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:38:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:38:47: #2 number of paired peaks: 1289 INFO @ Thu, 16 Apr 2020 03:38:47: start model_add_line... INFO @ Thu, 16 Apr 2020 03:38:47: start X-correlation... INFO @ Thu, 16 Apr 2020 03:38:47: end of X-cor INFO @ Thu, 16 Apr 2020 03:38:47: #2 finished! INFO @ Thu, 16 Apr 2020 03:38:47: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 03:38:47: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 03:38:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.20_model.r WARNING @ Thu, 16 Apr 2020 03:38:47: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:38:47: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 03:38:47: #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 03:38:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:38:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:38:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386749/SRX6386749.20_summits.bed INFO @ Thu, 16 Apr 2020 03:39:04: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (933 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。