Job ID = 2003500 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T03:15:05 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 4,960,806 reads read : 4,960,806 reads written : 4,960,806 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:01:55 4960806 reads; of these: 4960806 (100.00%) were unpaired; of these: 349277 (7.04%) aligned 0 times 3619329 (72.96%) aligned exactly 1 time 992200 (20.00%) aligned >1 times 92.96% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 597040 / 4611529 = 0.1295 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 12:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:20:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:20:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:20:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:20:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:20:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:20:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:20:31: 1000000 INFO @ Fri, 05 Jul 2019 12:20:33: 1000000 INFO @ Fri, 05 Jul 2019 12:20:35: 1000000 INFO @ Fri, 05 Jul 2019 12:20:39: 2000000 INFO @ Fri, 05 Jul 2019 12:20:43: 2000000 INFO @ Fri, 05 Jul 2019 12:20:46: 2000000 INFO @ Fri, 05 Jul 2019 12:20:47: 3000000 INFO @ Fri, 05 Jul 2019 12:20:54: 3000000 INFO @ Fri, 05 Jul 2019 12:20:54: 4000000 INFO @ Fri, 05 Jul 2019 12:20:54: #1 tag size is determined as 29 bps INFO @ Fri, 05 Jul 2019 12:20:54: #1 tag size = 29 INFO @ Fri, 05 Jul 2019 12:20:54: #1 total tags in treatment: 4014489 INFO @ Fri, 05 Jul 2019 12:20:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:20:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:20:54: #1 tags after filtering in treatment: 4014229 INFO @ Fri, 05 Jul 2019 12:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:20:54: #1 finished! INFO @ Fri, 05 Jul 2019 12:20:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:20:57: 3000000 INFO @ Fri, 05 Jul 2019 12:20:58: #2 number of paired peaks: 32277 INFO @ Fri, 05 Jul 2019 12:20:58: start model_add_line... INFO @ Fri, 05 Jul 2019 12:20:58: start X-correlation... INFO @ Fri, 05 Jul 2019 12:20:58: end of X-cor INFO @ Fri, 05 Jul 2019 12:20:58: #2 finished! INFO @ Fri, 05 Jul 2019 12:20:58: #2 predicted fragment length is 228 bps INFO @ Fri, 05 Jul 2019 12:20:58: #2 alternative fragment length(s) may be 228,271 bps INFO @ Fri, 05 Jul 2019 12:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.10_model.r INFO @ Fri, 05 Jul 2019 12:20:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:21:04: 4000000 INFO @ Fri, 05 Jul 2019 12:21:04: #1 tag size is determined as 29 bps INFO @ Fri, 05 Jul 2019 12:21:04: #1 tag size = 29 INFO @ Fri, 05 Jul 2019 12:21:04: #1 total tags in treatment: 4014489 INFO @ Fri, 05 Jul 2019 12:21:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:21:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:21:04: #1 tags after filtering in treatment: 4014229 INFO @ Fri, 05 Jul 2019 12:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:21:04: #1 finished! INFO @ Fri, 05 Jul 2019 12:21:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:21:07: #2 number of paired peaks: 32277 INFO @ Fri, 05 Jul 2019 12:21:07: start model_add_line... INFO @ Fri, 05 Jul 2019 12:21:07: start X-correlation... INFO @ Fri, 05 Jul 2019 12:21:07: 4000000 INFO @ Fri, 05 Jul 2019 12:21:07: end of X-cor INFO @ Fri, 05 Jul 2019 12:21:07: #2 finished! INFO @ Fri, 05 Jul 2019 12:21:07: #2 predicted fragment length is 228 bps INFO @ Fri, 05 Jul 2019 12:21:07: #2 alternative fragment length(s) may be 228,271 bps INFO @ Fri, 05 Jul 2019 12:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.05_model.r INFO @ Fri, 05 Jul 2019 12:21:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:21:07: #1 tag size is determined as 29 bps INFO @ Fri, 05 Jul 2019 12:21:07: #1 tag size = 29 INFO @ Fri, 05 Jul 2019 12:21:07: #1 total tags in treatment: 4014489 INFO @ Fri, 05 Jul 2019 12:21:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:21:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:21:07: #1 tags after filtering in treatment: 4014229 INFO @ Fri, 05 Jul 2019 12:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:21:07: #1 finished! INFO @ Fri, 05 Jul 2019 12:21:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:21:11: #2 number of paired peaks: 32277 INFO @ Fri, 05 Jul 2019 12:21:11: start model_add_line... INFO @ Fri, 05 Jul 2019 12:21:11: start X-correlation... INFO @ Fri, 05 Jul 2019 12:21:11: end of X-cor INFO @ Fri, 05 Jul 2019 12:21:11: #2 finished! INFO @ Fri, 05 Jul 2019 12:21:11: #2 predicted fragment length is 228 bps INFO @ Fri, 05 Jul 2019 12:21:11: #2 alternative fragment length(s) may be 228,271 bps INFO @ Fri, 05 Jul 2019 12:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.20_model.r INFO @ Fri, 05 Jul 2019 12:21:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:21:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.10_summits.bed INFO @ Fri, 05 Jul 2019 12:21:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:21:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:21:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.05_summits.bed INFO @ Fri, 05 Jul 2019 12:21:27: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204149/SRX204149.20_summits.bed INFO @ Fri, 05 Jul 2019 12:21:30: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (21 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。