Job ID = 2640701 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:20:16 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 ) 2019-08-24T09:20:16 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 ) 2019-08-24T09:20:16 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 ) 2019-08-24T09:20:17 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 ) 2019-08-24T09:20:17 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 ) 2019-08-24T09:20:17 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 ) 2019-08-24T09:27:18 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 ) 2019-08-24T09:27:18 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 ) 2019-08-24T09:27:18 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 : 27,263,887 reads read : 54,527,774 reads written : 27,263,887 reads 0-length : 27,263,887 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:11 27263887 reads; of these: 27263887 (100.00%) were unpaired; of these: 835183 (3.06%) aligned 0 times 22280317 (81.72%) aligned exactly 1 time 4148387 (15.22%) aligned >1 times 96.94% overall alignment rate Time searching: 00:19:12 Overall time: 00:19:12 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_sort_core] merging from 12 files... [bam_rmdupse_core] 1620161 / 26428704 = 0.0613 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.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 18:56:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:56:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:56:38: 1000000 INFO @ Sat, 24 Aug 2019 18:56:50: 2000000 INFO @ Sat, 24 Aug 2019 18:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.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 18:56:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:56:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:57:02: 3000000 INFO @ Sat, 24 Aug 2019 18:57:05: 1000000 INFO @ Sat, 24 Aug 2019 18:57:13: 4000000 INFO @ Sat, 24 Aug 2019 18:57:15: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:57:24: 3000000 INFO @ Sat, 24 Aug 2019 18:57:25: 5000000 INFO @ Sat, 24 Aug 2019 18:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.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 18:57:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:57:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:57:33: 4000000 INFO @ Sat, 24 Aug 2019 18:57:36: 1000000 INFO @ Sat, 24 Aug 2019 18:57:37: 6000000 INFO @ Sat, 24 Aug 2019 18:57:43: 5000000 INFO @ Sat, 24 Aug 2019 18:57:46: 2000000 INFO @ Sat, 24 Aug 2019 18:57:49: 7000000 INFO @ Sat, 24 Aug 2019 18:57:52: 6000000 INFO @ Sat, 24 Aug 2019 18:57:56: 3000000 INFO @ Sat, 24 Aug 2019 18:58:00: 8000000 INFO @ Sat, 24 Aug 2019 18:58:02: 7000000 INFO @ Sat, 24 Aug 2019 18:58:06: 4000000 INFO @ Sat, 24 Aug 2019 18:58:12: 8000000 INFO @ Sat, 24 Aug 2019 18:58:12: 9000000 INFO @ Sat, 24 Aug 2019 18:58:16: 5000000 INFO @ Sat, 24 Aug 2019 18:58:22: 9000000 INFO @ Sat, 24 Aug 2019 18:58:24: 10000000 INFO @ Sat, 24 Aug 2019 18:58:27: 6000000 INFO @ Sat, 24 Aug 2019 18:58:32: 10000000 INFO @ Sat, 24 Aug 2019 18:58:36: 11000000 INFO @ Sat, 24 Aug 2019 18:58:36: 7000000 INFO @ Sat, 24 Aug 2019 18:58:42: 11000000 INFO @ Sat, 24 Aug 2019 18:58:46: 8000000 INFO @ Sat, 24 Aug 2019 18:58:48: 12000000 INFO @ Sat, 24 Aug 2019 18:58:51: 12000000 INFO @ Sat, 24 Aug 2019 18:58:56: 9000000 INFO @ Sat, 24 Aug 2019 18:59:00: 13000000 INFO @ Sat, 24 Aug 2019 18:59:01: 13000000 INFO @ Sat, 24 Aug 2019 18:59:06: 10000000 INFO @ Sat, 24 Aug 2019 18:59:11: 14000000 INFO @ Sat, 24 Aug 2019 18:59:12: 14000000 INFO @ Sat, 24 Aug 2019 18:59:15: 11000000 INFO @ Sat, 24 Aug 2019 18:59:21: 15000000 INFO @ Sat, 24 Aug 2019 18:59:23: 15000000 INFO @ Sat, 24 Aug 2019 18:59:25: 12000000 INFO @ Sat, 24 Aug 2019 18:59:31: 16000000 INFO @ Sat, 24 Aug 2019 18:59:35: 16000000 INFO @ Sat, 24 Aug 2019 18:59:36: 13000000 INFO @ Sat, 24 Aug 2019 18:59:41: 17000000 INFO @ Sat, 24 Aug 2019 18:59:46: 14000000 INFO @ Sat, 24 Aug 2019 18:59:47: 17000000 INFO @ Sat, 24 Aug 2019 18:59:50: 18000000 INFO @ Sat, 24 Aug 2019 18:59:56: 15000000 INFO @ Sat, 24 Aug 2019 18:59:59: 18000000 INFO @ Sat, 24 Aug 2019 19:00:00: 19000000 INFO @ Sat, 24 Aug 2019 19:00:06: 16000000 INFO @ Sat, 24 Aug 2019 19:00:10: 20000000 INFO @ Sat, 24 Aug 2019 19:00:11: 19000000 INFO @ Sat, 24 Aug 2019 19:00:16: 17000000 INFO @ Sat, 24 Aug 2019 19:00:20: 21000000 INFO @ Sat, 24 Aug 2019 19:00:22: 20000000 INFO @ Sat, 24 Aug 2019 19:00:26: 18000000 INFO @ Sat, 24 Aug 2019 19:00:29: 22000000 INFO @ Sat, 24 Aug 2019 19:00:34: 21000000 INFO @ Sat, 24 Aug 2019 19:00:36: 19000000 INFO @ Sat, 24 Aug 2019 19:00:39: 23000000 INFO @ Sat, 24 Aug 2019 19:00:45: 22000000 INFO @ Sat, 24 Aug 2019 19:00:46: 20000000 INFO @ Sat, 24 Aug 2019 19:00:49: 24000000 INFO @ Sat, 24 Aug 2019 19:00:56: 21000000 INFO @ Sat, 24 Aug 2019 19:00:57: 23000000 INFO @ Sat, 24 Aug 2019 19:00:58: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:00:58: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:00:58: #1 total tags in treatment: 24808543 INFO @ Sat, 24 Aug 2019 19:00:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:00:58: #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 19:00:58: #1 tags after filtering in treatment: 24808315 INFO @ Sat, 24 Aug 2019 19:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:00:58: #1 finished! INFO @ Sat, 24 Aug 2019 19:00:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:06: 22000000 INFO @ Sat, 24 Aug 2019 19:01:06: #2 number of paired peaks: 122474 INFO @ Sat, 24 Aug 2019 19:01:06: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:07: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:07: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:07: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:07: #2 predicted fragment length is 205 bps INFO @ Sat, 24 Aug 2019 19:01:07: #2 alternative fragment length(s) may be 4,205 bps INFO @ Sat, 24 Aug 2019 19:01:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.10_model.r INFO @ Sat, 24 Aug 2019 19:01:07: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:01:09: 24000000 INFO @ Sat, 24 Aug 2019 19:01:15: 23000000 INFO @ Sat, 24 Aug 2019 19:01:18: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:01:18: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:01:18: #1 total tags in treatment: 24808543 INFO @ Sat, 24 Aug 2019 19:01:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:01:18: #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 19:01:19: #1 tags after filtering in treatment: 24808315 INFO @ Sat, 24 Aug 2019 19:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:01:19: #1 finished! INFO @ Sat, 24 Aug 2019 19:01:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:25: 24000000 INFO @ Sat, 24 Aug 2019 19:01:27: #2 number of paired peaks: 122474 INFO @ Sat, 24 Aug 2019 19:01:27: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:27: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:27: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:27: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:27: #2 predicted fragment length is 205 bps INFO @ Sat, 24 Aug 2019 19:01:27: #2 alternative fragment length(s) may be 4,205 bps INFO @ Sat, 24 Aug 2019 19:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.05_model.r INFO @ Sat, 24 Aug 2019 19:01:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:01:33: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:01:33: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:01:33: #1 total tags in treatment: 24808543 INFO @ Sat, 24 Aug 2019 19:01:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:01:33: #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 19:01:33: #1 tags after filtering in treatment: 24808315 INFO @ Sat, 24 Aug 2019 19:01:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:01:33: #1 finished! INFO @ Sat, 24 Aug 2019 19:01:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:41: #2 number of paired peaks: 122474 INFO @ Sat, 24 Aug 2019 19:01:41: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:42: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:42: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:42: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:42: #2 predicted fragment length is 205 bps INFO @ Sat, 24 Aug 2019 19:01:42: #2 alternative fragment length(s) may be 4,205 bps INFO @ Sat, 24 Aug 2019 19:01:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.20_model.r INFO @ Sat, 24 Aug 2019 19:01:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:02:37: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:02:59: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:03:11: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.10_summits.bed INFO @ Sat, 24 Aug 2019 19:03:26: Done! pass1 - making usageList (89 chroms): 8 millis pass2 - checking and writing primary data (17419 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:03:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:03:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:03:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.05_summits.bed INFO @ Sat, 24 Aug 2019 19:03:46: Done! pass1 - making usageList (130 chroms): 8 millis pass2 - checking and writing primary data (35346 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:03:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:03:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375058/SRX5375058.20_summits.bed INFO @ Sat, 24 Aug 2019 19:03:58: Done! pass1 - making usageList (42 chroms): 4 millis pass2 - checking and writing primary data (4561 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。