Job ID = 4303039 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,790,193 reads read : 26,790,193 reads written : 26,790,193 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198436.sra.cache’: 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: 00:05:43 26790193 reads; of these: 26790193 (100.00%) were unpaired; of these: 2346333 (8.76%) aligned 0 times 20142335 (75.19%) aligned exactly 1 time 4301525 (16.06%) aligned >1 times 91.24% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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 12 files... [bam_rmdupse_core] 14429494 / 24443860 = 0.5903 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.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 @ Thu, 12 Dec 2019 00:46:05: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:46:05: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:46:11: 1000000 INFO @ Thu, 12 Dec 2019 00:46:16: 2000000 INFO @ Thu, 12 Dec 2019 00:46:22: 3000000 INFO @ Thu, 12 Dec 2019 00:46:27: 4000000 INFO @ Thu, 12 Dec 2019 00:46:33: 5000000 INFO @ Thu, 12 Dec 2019 00:46:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.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 @ Thu, 12 Dec 2019 00:46:34: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:46:34: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:46:39: 6000000 INFO @ Thu, 12 Dec 2019 00:46:40: 1000000 INFO @ Thu, 12 Dec 2019 00:46:44: 7000000 INFO @ Thu, 12 Dec 2019 00:46:47: 2000000 INFO @ Thu, 12 Dec 2019 00:46:50: 8000000 INFO @ Thu, 12 Dec 2019 00:46:53: 3000000 INFO @ Thu, 12 Dec 2019 00:46:56: 9000000 INFO @ Thu, 12 Dec 2019 00:47:00: 4000000 INFO @ Thu, 12 Dec 2019 00:47:01: 10000000 INFO @ Thu, 12 Dec 2019 00:47:02: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:47:02: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:47:02: #1 total tags in treatment: 10014366 INFO @ Thu, 12 Dec 2019 00:47:02: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:47:02: #1 tags after filtering in treatment: 10014366 INFO @ Thu, 12 Dec 2019 00:47:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:02: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:02: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:02: #2 number of paired peaks: 928 WARNING @ Thu, 12 Dec 2019 00:47:02: Fewer paired peaks (928) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 928 pairs to build model! INFO @ Thu, 12 Dec 2019 00:47:02: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:03: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:03: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:03: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:03: #2 predicted fragment length is 117 bps INFO @ Thu, 12 Dec 2019 00:47:03: #2 alternative fragment length(s) may be 117,597 bps INFO @ Thu, 12 Dec 2019 00:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.05_model.r INFO @ Thu, 12 Dec 2019 00:47:03: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.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 @ Thu, 12 Dec 2019 00:47:04: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:04: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:06: 5000000 INFO @ Thu, 12 Dec 2019 00:47:11: 1000000 INFO @ Thu, 12 Dec 2019 00:47:13: 6000000 INFO @ Thu, 12 Dec 2019 00:47:17: 2000000 INFO @ Thu, 12 Dec 2019 00:47:19: 7000000 INFO @ Thu, 12 Dec 2019 00:47:23: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:24: 3000000 INFO @ Thu, 12 Dec 2019 00:47:26: 8000000 INFO @ Thu, 12 Dec 2019 00:47:30: 4000000 INFO @ Thu, 12 Dec 2019 00:47:32: 9000000 INFO @ Thu, 12 Dec 2019 00:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.05_summits.bed INFO @ Thu, 12 Dec 2019 00:47:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5343 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:47:37: 5000000 INFO @ Thu, 12 Dec 2019 00:47:39: 10000000 INFO @ Thu, 12 Dec 2019 00:47:39: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:47:39: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:47:39: #1 total tags in treatment: 10014366 INFO @ Thu, 12 Dec 2019 00:47:39: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:47:39: #1 tags after filtering in treatment: 10014366 INFO @ Thu, 12 Dec 2019 00:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:39: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:39: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:40: #2 number of paired peaks: 928 WARNING @ Thu, 12 Dec 2019 00:47:40: Fewer paired peaks (928) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 928 pairs to build model! INFO @ Thu, 12 Dec 2019 00:47:40: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:40: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:40: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:40: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:40: #2 predicted fragment length is 117 bps INFO @ Thu, 12 Dec 2019 00:47:40: #2 alternative fragment length(s) may be 117,597 bps INFO @ Thu, 12 Dec 2019 00:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.10_model.r INFO @ Thu, 12 Dec 2019 00:47:40: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:43: 6000000 INFO @ Thu, 12 Dec 2019 00:47:49: 7000000 INFO @ Thu, 12 Dec 2019 00:47:55: 8000000 INFO @ Thu, 12 Dec 2019 00:48:01: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:48:01: 9000000 INFO @ Thu, 12 Dec 2019 00:48:07: 10000000 INFO @ Thu, 12 Dec 2019 00:48:08: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:48:08: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:48:08: #1 total tags in treatment: 10014366 INFO @ Thu, 12 Dec 2019 00:48:08: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:48:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:48:08: #1 tags after filtering in treatment: 10014366 INFO @ Thu, 12 Dec 2019 00:48:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:48:08: #1 finished! INFO @ Thu, 12 Dec 2019 00:48:08: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:48:09: #2 number of paired peaks: 928 WARNING @ Thu, 12 Dec 2019 00:48:09: Fewer paired peaks (928) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 928 pairs to build model! INFO @ Thu, 12 Dec 2019 00:48:09: start model_add_line... INFO @ Thu, 12 Dec 2019 00:48:09: start X-correlation... INFO @ Thu, 12 Dec 2019 00:48:09: end of X-cor INFO @ Thu, 12 Dec 2019 00:48:09: #2 finished! INFO @ Thu, 12 Dec 2019 00:48:09: #2 predicted fragment length is 117 bps INFO @ Thu, 12 Dec 2019 00:48:09: #2 alternative fragment length(s) may be 117,597 bps INFO @ Thu, 12 Dec 2019 00:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.20_model.r INFO @ Thu, 12 Dec 2019 00:48:09: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.10_summits.bed INFO @ Thu, 12 Dec 2019 00:48:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3408 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:48:29: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494904/SRX494904.20_summits.bed INFO @ Thu, 12 Dec 2019 00:48:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1772 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。