Job ID = 2640487 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:18:01 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 ) 2019-08-24T08:21:52 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 : 10,503,219 reads read : 21,006,438 reads written : 10,503,219 reads 0-length : 10,503,219 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: 00:09:07 10503219 reads; of these: 10503219 (100.00%) were unpaired; of these: 902297 (8.59%) aligned 0 times 7113301 (67.72%) aligned exactly 1 time 2487621 (23.68%) aligned >1 times 91.41% overall alignment rate Time searching: 00:09:07 Overall time: 00:09:07 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] 897133 / 9600922 = 0.0934 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.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 17:36:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:36:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:36:33: 1000000 INFO @ Sat, 24 Aug 2019 17:36:41: 2000000 INFO @ Sat, 24 Aug 2019 17:36:48: 3000000 INFO @ Sat, 24 Aug 2019 17:36:55: 4000000 INFO @ Sat, 24 Aug 2019 17:36:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.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 17:36:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:36:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:37:02: 5000000 INFO @ Sat, 24 Aug 2019 17:37:04: 1000000 INFO @ Sat, 24 Aug 2019 17:37:09: 6000000 INFO @ Sat, 24 Aug 2019 17:37:11: 2000000 INFO @ Sat, 24 Aug 2019 17:37:17: 7000000 INFO @ Sat, 24 Aug 2019 17:37:18: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:37:25: 4000000 INFO @ Sat, 24 Aug 2019 17:37:26: 8000000 INFO @ Sat, 24 Aug 2019 17:37:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.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 17:37:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:37:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:37:32: 5000000 INFO @ Sat, 24 Aug 2019 17:37:32: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:37:32: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:37:32: #1 total tags in treatment: 8703789 INFO @ Sat, 24 Aug 2019 17:37:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:37:32: #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 17:37:33: #1 tags after filtering in treatment: 8703564 INFO @ Sat, 24 Aug 2019 17:37:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:37:33: #1 finished! INFO @ Sat, 24 Aug 2019 17:37:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:37:34: 1000000 INFO @ Sat, 24 Aug 2019 17:37:35: #2 number of paired peaks: 20421 INFO @ Sat, 24 Aug 2019 17:37:35: start model_add_line... INFO @ Sat, 24 Aug 2019 17:37:35: start X-correlation... INFO @ Sat, 24 Aug 2019 17:37:35: end of X-cor INFO @ Sat, 24 Aug 2019 17:37:35: #2 finished! INFO @ Sat, 24 Aug 2019 17:37:35: #2 predicted fragment length is 134 bps INFO @ Sat, 24 Aug 2019 17:37:35: #2 alternative fragment length(s) may be 134 bps INFO @ Sat, 24 Aug 2019 17:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.05_model.r INFO @ Sat, 24 Aug 2019 17:37:35: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:37:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:37:39: 6000000 INFO @ Sat, 24 Aug 2019 17:37:41: 2000000 INFO @ Sat, 24 Aug 2019 17:37:46: 7000000 INFO @ Sat, 24 Aug 2019 17:37:49: 3000000 INFO @ Sat, 24 Aug 2019 17:37:53: 8000000 INFO @ Sat, 24 Aug 2019 17:37:55: 4000000 INFO @ Sat, 24 Aug 2019 17:37:59: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:37:59: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:37:59: #1 total tags in treatment: 8703789 INFO @ Sat, 24 Aug 2019 17:37:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:37:59: #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 17:37:59: #1 tags after filtering in treatment: 8703564 INFO @ Sat, 24 Aug 2019 17:37:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:37:59: #1 finished! INFO @ Sat, 24 Aug 2019 17:37:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:38:01: #2 number of paired peaks: 20421 INFO @ Sat, 24 Aug 2019 17:38:01: start model_add_line... INFO @ Sat, 24 Aug 2019 17:38:01: start X-correlation... INFO @ Sat, 24 Aug 2019 17:38:01: end of X-cor INFO @ Sat, 24 Aug 2019 17:38:01: #2 finished! INFO @ Sat, 24 Aug 2019 17:38:01: #2 predicted fragment length is 134 bps INFO @ Sat, 24 Aug 2019 17:38:01: #2 alternative fragment length(s) may be 134 bps INFO @ Sat, 24 Aug 2019 17:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.10_model.r INFO @ Sat, 24 Aug 2019 17:38:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:38:02: 5000000 INFO @ Sat, 24 Aug 2019 17:38:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:38:08: 6000000 INFO @ Sat, 24 Aug 2019 17:38:15: 7000000 INFO @ Sat, 24 Aug 2019 17:38:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:38:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:38:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.05_summits.bed INFO @ Sat, 24 Aug 2019 17:38:17: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (3859 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:38:22: 8000000 INFO @ Sat, 24 Aug 2019 17:38:26: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:38:26: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:38:26: #1 total tags in treatment: 8703789 INFO @ Sat, 24 Aug 2019 17:38:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:38:26: #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 17:38:27: #1 tags after filtering in treatment: 8703564 INFO @ Sat, 24 Aug 2019 17:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:38:27: #1 finished! INFO @ Sat, 24 Aug 2019 17:38:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:38:29: #2 number of paired peaks: 20421 INFO @ Sat, 24 Aug 2019 17:38:29: start model_add_line... INFO @ Sat, 24 Aug 2019 17:38:29: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:38:29: start X-correlation... INFO @ Sat, 24 Aug 2019 17:38:29: end of X-cor INFO @ Sat, 24 Aug 2019 17:38:29: #2 finished! INFO @ Sat, 24 Aug 2019 17:38:29: #2 predicted fragment length is 134 bps INFO @ Sat, 24 Aug 2019 17:38:29: #2 alternative fragment length(s) may be 134 bps INFO @ Sat, 24 Aug 2019 17:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.20_model.r INFO @ Sat, 24 Aug 2019 17:38:29: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:38:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.10_summits.bed INFO @ Sat, 24 Aug 2019 17:38:43: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (1139 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:38:57: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374996/SRX5374996.20_summits.bed INFO @ Sat, 24 Aug 2019 17:39:11: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。