Job ID = 5720237 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,128,664 reads read : 19,128,664 reads written : 19,128,664 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: 00:04:15 19128664 reads; of these: 19128664 (100.00%) were unpaired; of these: 370034 (1.93%) aligned 0 times 16018701 (83.74%) aligned exactly 1 time 2739929 (14.32%) aligned >1 times 98.07% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6320058 / 18758630 = 0.3369 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 @ Wed, 15 Apr 2020 22:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:47:08: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:47:08: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:47:14: 1000000 INFO @ Wed, 15 Apr 2020 22:47:20: 2000000 INFO @ Wed, 15 Apr 2020 22:47:26: 3000000 INFO @ Wed, 15 Apr 2020 22:47:32: 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 @ Wed, 15 Apr 2020 22:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:47:38: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:47:38: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:47:38: 5000000 INFO @ Wed, 15 Apr 2020 22:47:44: 1000000 INFO @ Wed, 15 Apr 2020 22:47:45: 6000000 INFO @ Wed, 15 Apr 2020 22:47:50: 2000000 INFO @ Wed, 15 Apr 2020 22:47:51: 7000000 INFO @ Wed, 15 Apr 2020 22:47:56: 3000000 INFO @ Wed, 15 Apr 2020 22:47:57: 8000000 INFO @ Wed, 15 Apr 2020 22:48:02: 4000000 INFO @ Wed, 15 Apr 2020 22:48:03: 9000000 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 @ Wed, 15 Apr 2020 22:48:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:48:08: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:48:08: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:48:08: 5000000 INFO @ Wed, 15 Apr 2020 22:48:09: 10000000 INFO @ Wed, 15 Apr 2020 22:48:13: 1000000 INFO @ Wed, 15 Apr 2020 22:48:15: 6000000 INFO @ Wed, 15 Apr 2020 22:48:15: 11000000 INFO @ Wed, 15 Apr 2020 22:48:18: 2000000 INFO @ Wed, 15 Apr 2020 22:48:21: 7000000 INFO @ Wed, 15 Apr 2020 22:48:21: 12000000 INFO @ Wed, 15 Apr 2020 22:48:23: 3000000 INFO @ Wed, 15 Apr 2020 22:48:24: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:48:24: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:48:24: #1 total tags in treatment: 12438572 INFO @ Wed, 15 Apr 2020 22:48:24: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:48:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:48:24: #1 tags after filtering in treatment: 12438572 INFO @ Wed, 15 Apr 2020 22:48:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:48:24: #1 finished! INFO @ Wed, 15 Apr 2020 22:48:24: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:48:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:48:25: #2 number of paired peaks: 1499 INFO @ Wed, 15 Apr 2020 22:48:25: start model_add_line... INFO @ Wed, 15 Apr 2020 22:48:25: start X-correlation... INFO @ Wed, 15 Apr 2020 22:48:25: end of X-cor INFO @ Wed, 15 Apr 2020 22:48:25: #2 finished! INFO @ Wed, 15 Apr 2020 22:48:25: #2 predicted fragment length is 163 bps INFO @ Wed, 15 Apr 2020 22:48:25: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 15 Apr 2020 22:48:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.05_model.r INFO @ Wed, 15 Apr 2020 22:48:25: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:48:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:48:27: 8000000 INFO @ Wed, 15 Apr 2020 22:48:28: 4000000 INFO @ Wed, 15 Apr 2020 22:48:33: 9000000 INFO @ Wed, 15 Apr 2020 22:48:33: 5000000 INFO @ Wed, 15 Apr 2020 22:48:38: 6000000 INFO @ Wed, 15 Apr 2020 22:48:39: 10000000 INFO @ Wed, 15 Apr 2020 22:48:44: 7000000 INFO @ Wed, 15 Apr 2020 22:48:45: 11000000 INFO @ Wed, 15 Apr 2020 22:48:49: 8000000 INFO @ Wed, 15 Apr 2020 22:48:52: 12000000 INFO @ Wed, 15 Apr 2020 22:48:54: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:48:54: 9000000 INFO @ Wed, 15 Apr 2020 22:48:55: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:48:55: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:48:55: #1 total tags in treatment: 12438572 INFO @ Wed, 15 Apr 2020 22:48:55: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:48:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:48:55: #1 tags after filtering in treatment: 12438572 INFO @ Wed, 15 Apr 2020 22:48:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:48:55: #1 finished! INFO @ Wed, 15 Apr 2020 22:48:55: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:48:56: #2 number of paired peaks: 1499 INFO @ Wed, 15 Apr 2020 22:48:56: start model_add_line... INFO @ Wed, 15 Apr 2020 22:48:56: start X-correlation... INFO @ Wed, 15 Apr 2020 22:48:56: end of X-cor INFO @ Wed, 15 Apr 2020 22:48:56: #2 finished! INFO @ Wed, 15 Apr 2020 22:48:56: #2 predicted fragment length is 163 bps INFO @ Wed, 15 Apr 2020 22:48:56: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 15 Apr 2020 22:48:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.10_model.r INFO @ Wed, 15 Apr 2020 22:48:56: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:48:59: 10000000 INFO @ Wed, 15 Apr 2020 22:49:04: 11000000 INFO @ Wed, 15 Apr 2020 22:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.05_summits.bed INFO @ Wed, 15 Apr 2020 22:49:09: Done! INFO @ Wed, 15 Apr 2020 22:49:09: 12000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5351 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:49:11: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:49:11: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:49:11: #1 total tags in treatment: 12438572 INFO @ Wed, 15 Apr 2020 22:49:11: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:49:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:49:11: #1 tags after filtering in treatment: 12438572 INFO @ Wed, 15 Apr 2020 22:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:49:11: #1 finished! INFO @ Wed, 15 Apr 2020 22:49:11: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:49:12: #2 number of paired peaks: 1499 INFO @ Wed, 15 Apr 2020 22:49:12: start model_add_line... INFO @ Wed, 15 Apr 2020 22:49:12: start X-correlation... INFO @ Wed, 15 Apr 2020 22:49:12: end of X-cor INFO @ Wed, 15 Apr 2020 22:49:12: #2 finished! INFO @ Wed, 15 Apr 2020 22:49:12: #2 predicted fragment length is 163 bps INFO @ Wed, 15 Apr 2020 22:49:12: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 15 Apr 2020 22:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.20_model.r INFO @ Wed, 15 Apr 2020 22:49:12: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:49:28: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:49:40: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.10_summits.bed INFO @ Wed, 15 Apr 2020 22:49:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3523 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:49:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:49:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:49:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720169/SRX6720169.20_summits.bed INFO @ Wed, 15 Apr 2020 22:49:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1849 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。