Job ID = 2640583 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:52:38 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 ) 2019-08-24T08:52:38 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 : 5,834,651 reads read : 11,669,302 reads written : 5,834,651 reads 0-length : 5,834,651 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:45 5834651 reads; of these: 5834651 (100.00%) were unpaired; of these: 350046 (6.00%) aligned 0 times 4064552 (69.66%) aligned exactly 1 time 1420053 (24.34%) aligned >1 times 94.00% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 201024 / 5484605 = 0.0367 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:01:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.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 @ Sat, 24 Aug 2019 18:01:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:01:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:01:18: 1000000 INFO @ Sat, 24 Aug 2019 18:01:26: 2000000 INFO @ Sat, 24 Aug 2019 18:01:34: 3000000 INFO @ Sat, 24 Aug 2019 18:01:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.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 @ Sat, 24 Aug 2019 18:01:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:01:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:01:43: 4000000 INFO @ Sat, 24 Aug 2019 18:01:48: 1000000 INFO @ Sat, 24 Aug 2019 18:01:51: 5000000 INFO @ Sat, 24 Aug 2019 18:01:54: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:01:54: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:01:54: #1 total tags in treatment: 5283581 INFO @ Sat, 24 Aug 2019 18:01:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:01:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:01:54: #1 tags after filtering in treatment: 5283330 INFO @ Sat, 24 Aug 2019 18:01:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:01:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:01:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:01:56: #2 number of paired peaks: 21887 INFO @ Sat, 24 Aug 2019 18:01:56: start model_add_line... INFO @ Sat, 24 Aug 2019 18:01:56: start X-correlation... INFO @ Sat, 24 Aug 2019 18:01:56: end of X-cor INFO @ Sat, 24 Aug 2019 18:01:56: #2 finished! INFO @ Sat, 24 Aug 2019 18:01:56: #2 predicted fragment length is 199 bps INFO @ Sat, 24 Aug 2019 18:01:56: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 24 Aug 2019 18:01:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.05_model.r INFO @ Sat, 24 Aug 2019 18:01:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:01:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:01:57: 2000000 INFO @ Sat, 24 Aug 2019 18:02:05: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:02:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.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 @ Sat, 24 Aug 2019 18:02:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:02:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:02:14: 4000000 INFO @ Sat, 24 Aug 2019 18:02:14: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:02:18: 1000000 INFO @ Sat, 24 Aug 2019 18:02:22: 5000000 INFO @ Sat, 24 Aug 2019 18:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.05_summits.bed INFO @ Sat, 24 Aug 2019 18:02:24: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:02:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:02:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:02:25: #1 total tags in treatment: 5283581 INFO @ Sat, 24 Aug 2019 18:02:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:02:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:02:25: #1 tags after filtering in treatment: 5283330 INFO @ Sat, 24 Aug 2019 18:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:02:25: #1 finished! INFO @ Sat, 24 Aug 2019 18:02:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:02:27: 2000000 INFO @ Sat, 24 Aug 2019 18:02:27: #2 number of paired peaks: 21887 INFO @ Sat, 24 Aug 2019 18:02:27: start model_add_line... INFO @ Sat, 24 Aug 2019 18:02:27: start X-correlation... INFO @ Sat, 24 Aug 2019 18:02:27: end of X-cor INFO @ Sat, 24 Aug 2019 18:02:27: #2 finished! INFO @ Sat, 24 Aug 2019 18:02:27: #2 predicted fragment length is 199 bps INFO @ Sat, 24 Aug 2019 18:02:27: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 24 Aug 2019 18:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.10_model.r INFO @ Sat, 24 Aug 2019 18:02:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:02:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:02:35: 3000000 INFO @ Sat, 24 Aug 2019 18:02:44: 4000000 INFO @ Sat, 24 Aug 2019 18:02:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:02:52: 5000000 INFO @ Sat, 24 Aug 2019 18:02:55: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:02:55: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:02:55: #1 total tags in treatment: 5283581 INFO @ Sat, 24 Aug 2019 18:02:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:02:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:02:55: #1 tags after filtering in treatment: 5283330 INFO @ Sat, 24 Aug 2019 18:02:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:02:55: #1 finished! INFO @ Sat, 24 Aug 2019 18:02:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:02:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:02:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:02:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:02:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.10_summits.bed INFO @ Sat, 24 Aug 2019 18:02:56: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:02:57: #2 number of paired peaks: 21887 INFO @ Sat, 24 Aug 2019 18:02:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:02:58: start X-correlation... INFO @ Sat, 24 Aug 2019 18:02:58: end of X-cor INFO @ Sat, 24 Aug 2019 18:02:58: #2 finished! INFO @ Sat, 24 Aug 2019 18:02:58: #2 predicted fragment length is 199 bps INFO @ Sat, 24 Aug 2019 18:02:58: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 24 Aug 2019 18:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.20_model.r INFO @ Sat, 24 Aug 2019 18:02:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:03:16: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375022/SRX5375022.20_summits.bed INFO @ Sat, 24 Aug 2019 18:03:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (77 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。