Job ID = 2001173 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:31:29 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 ) 2019-07-04T19:36:11 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 ) 2019-07-04T19:41:48 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 ) 2019-07-04T19:43:07 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 : 113,799,543 reads read : 113,799,543 reads written : 113,799,543 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:02:08 113799543 reads; of these: 113799543 (100.00%) were unpaired; of these: 2052163 (1.80%) aligned 0 times 100051485 (87.92%) aligned exactly 1 time 11695895 (10.28%) aligned >1 times 98.20% overall alignment rate Time searching: 01:02:10 Overall time: 01:02:10 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 48 files... [bam_rmdupse_core] 76752983 / 111747380 = 0.6868 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 06:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.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 06:27:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:27:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:28:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.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 06:28:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:28:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.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 06:28:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:28:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:28:08: 1000000 INFO @ Fri, 05 Jul 2019 06:28:10: 1000000 INFO @ Fri, 05 Jul 2019 06:28:12: 1000000 INFO @ Fri, 05 Jul 2019 06:28:17: 2000000 INFO @ Fri, 05 Jul 2019 06:28:21: 2000000 INFO @ Fri, 05 Jul 2019 06:28:22: 2000000 INFO @ Fri, 05 Jul 2019 06:28:27: 3000000 INFO @ Fri, 05 Jul 2019 06:28:32: 3000000 INFO @ Fri, 05 Jul 2019 06:28:33: 3000000 INFO @ Fri, 05 Jul 2019 06:28:36: 4000000 INFO @ Fri, 05 Jul 2019 06:28:43: 4000000 INFO @ Fri, 05 Jul 2019 06:28:43: 4000000 INFO @ Fri, 05 Jul 2019 06:28:46: 5000000 INFO @ Fri, 05 Jul 2019 06:28:54: 5000000 INFO @ Fri, 05 Jul 2019 06:28:55: 5000000 INFO @ Fri, 05 Jul 2019 06:28:56: 6000000 INFO @ Fri, 05 Jul 2019 06:29:04: 6000000 INFO @ Fri, 05 Jul 2019 06:29:05: 6000000 INFO @ Fri, 05 Jul 2019 06:29:06: 7000000 INFO @ Fri, 05 Jul 2019 06:29:14: 7000000 INFO @ Fri, 05 Jul 2019 06:29:15: 8000000 INFO @ Fri, 05 Jul 2019 06:29:16: 7000000 INFO @ Fri, 05 Jul 2019 06:29:24: 8000000 INFO @ Fri, 05 Jul 2019 06:29:26: 9000000 INFO @ Fri, 05 Jul 2019 06:29:27: 8000000 INFO @ Fri, 05 Jul 2019 06:29:35: 9000000 INFO @ Fri, 05 Jul 2019 06:29:36: 10000000 INFO @ Fri, 05 Jul 2019 06:29:37: 9000000 INFO @ Fri, 05 Jul 2019 06:29:45: 10000000 INFO @ Fri, 05 Jul 2019 06:29:45: 11000000 INFO @ Fri, 05 Jul 2019 06:29:48: 10000000 INFO @ Fri, 05 Jul 2019 06:29:55: 12000000 INFO @ Fri, 05 Jul 2019 06:29:55: 11000000 INFO @ Fri, 05 Jul 2019 06:29:58: 11000000 INFO @ Fri, 05 Jul 2019 06:30:05: 13000000 INFO @ Fri, 05 Jul 2019 06:30:05: 12000000 INFO @ Fri, 05 Jul 2019 06:30:09: 12000000 INFO @ Fri, 05 Jul 2019 06:30:14: 14000000 INFO @ Fri, 05 Jul 2019 06:30:16: 13000000 INFO @ Fri, 05 Jul 2019 06:30:19: 13000000 INFO @ Fri, 05 Jul 2019 06:30:25: 15000000 INFO @ Fri, 05 Jul 2019 06:30:26: 14000000 INFO @ Fri, 05 Jul 2019 06:30:29: 14000000 INFO @ Fri, 05 Jul 2019 06:30:34: 16000000 INFO @ Fri, 05 Jul 2019 06:30:36: 15000000 INFO @ Fri, 05 Jul 2019 06:30:40: 15000000 INFO @ Fri, 05 Jul 2019 06:30:44: 17000000 INFO @ Fri, 05 Jul 2019 06:30:46: 16000000 INFO @ Fri, 05 Jul 2019 06:30:50: 16000000 INFO @ Fri, 05 Jul 2019 06:30:53: 18000000 INFO @ Fri, 05 Jul 2019 06:30:56: 17000000 INFO @ Fri, 05 Jul 2019 06:31:00: 17000000 INFO @ Fri, 05 Jul 2019 06:31:03: 19000000 INFO @ Fri, 05 Jul 2019 06:31:06: 18000000 INFO @ Fri, 05 Jul 2019 06:31:11: 18000000 INFO @ Fri, 05 Jul 2019 06:31:12: 20000000 INFO @ Fri, 05 Jul 2019 06:31:16: 19000000 INFO @ Fri, 05 Jul 2019 06:31:21: 19000000 INFO @ Fri, 05 Jul 2019 06:31:23: 21000000 INFO @ Fri, 05 Jul 2019 06:31:26: 20000000 INFO @ Fri, 05 Jul 2019 06:31:31: 20000000 INFO @ Fri, 05 Jul 2019 06:31:32: 22000000 INFO @ Fri, 05 Jul 2019 06:31:36: 21000000 INFO @ Fri, 05 Jul 2019 06:31:41: 21000000 INFO @ Fri, 05 Jul 2019 06:31:42: 23000000 INFO @ Fri, 05 Jul 2019 06:31:46: 22000000 INFO @ Fri, 05 Jul 2019 06:31:51: 24000000 INFO @ Fri, 05 Jul 2019 06:31:51: 22000000 INFO @ Fri, 05 Jul 2019 06:31:56: 23000000 INFO @ Fri, 05 Jul 2019 06:32:00: 25000000 INFO @ Fri, 05 Jul 2019 06:32:01: 23000000 INFO @ Fri, 05 Jul 2019 06:32:06: 24000000 INFO @ Fri, 05 Jul 2019 06:32:09: 26000000 INFO @ Fri, 05 Jul 2019 06:32:11: 24000000 INFO @ Fri, 05 Jul 2019 06:32:16: 25000000 INFO @ Fri, 05 Jul 2019 06:32:18: 27000000 INFO @ Fri, 05 Jul 2019 06:32:22: 25000000 INFO @ Fri, 05 Jul 2019 06:32:26: 26000000 INFO @ Fri, 05 Jul 2019 06:32:27: 28000000 INFO @ Fri, 05 Jul 2019 06:32:32: 26000000 INFO @ Fri, 05 Jul 2019 06:32:36: 29000000 INFO @ Fri, 05 Jul 2019 06:32:37: 27000000 INFO @ Fri, 05 Jul 2019 06:32:43: 27000000 INFO @ Fri, 05 Jul 2019 06:32:45: 30000000 INFO @ Fri, 05 Jul 2019 06:32:47: 28000000 INFO @ Fri, 05 Jul 2019 06:32:53: 28000000 INFO @ Fri, 05 Jul 2019 06:32:54: 31000000 INFO @ Fri, 05 Jul 2019 06:32:57: 29000000 INFO @ Fri, 05 Jul 2019 06:33:04: 32000000 INFO @ Fri, 05 Jul 2019 06:33:04: 29000000 INFO @ Fri, 05 Jul 2019 06:33:08: 30000000 INFO @ Fri, 05 Jul 2019 06:33:13: 33000000 INFO @ Fri, 05 Jul 2019 06:33:14: 30000000 INFO @ Fri, 05 Jul 2019 06:33:17: 31000000 INFO @ Fri, 05 Jul 2019 06:33:24: 34000000 INFO @ Fri, 05 Jul 2019 06:33:24: 31000000 INFO @ Fri, 05 Jul 2019 06:33:28: 32000000 INFO @ Fri, 05 Jul 2019 06:33:34: 32000000 INFO @ Fri, 05 Jul 2019 06:33:34: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:33:34: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:33:34: #1 total tags in treatment: 34994397 INFO @ Fri, 05 Jul 2019 06:33:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:33:34: #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 06:33:35: #1 tags after filtering in treatment: 34994199 INFO @ Fri, 05 Jul 2019 06:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:33:35: #1 finished! INFO @ Fri, 05 Jul 2019 06:33:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:33:37: 33000000 INFO @ Fri, 05 Jul 2019 06:33:44: 33000000 INFO @ Fri, 05 Jul 2019 06:33:44: #2 number of paired peaks: 66038 INFO @ Fri, 05 Jul 2019 06:33:44: start model_add_line... INFO @ Fri, 05 Jul 2019 06:33:45: start X-correlation... INFO @ Fri, 05 Jul 2019 06:33:45: end of X-cor INFO @ Fri, 05 Jul 2019 06:33:45: #2 finished! INFO @ Fri, 05 Jul 2019 06:33:45: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:33:45: #2 alternative fragment length(s) may be 4,134 bps INFO @ Fri, 05 Jul 2019 06:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.05_model.r INFO @ Fri, 05 Jul 2019 06:33:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:33:47: 34000000 INFO @ Fri, 05 Jul 2019 06:33:53: 34000000 INFO @ Fri, 05 Jul 2019 06:33:57: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:33:57: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:33:57: #1 total tags in treatment: 34994397 INFO @ Fri, 05 Jul 2019 06:33:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:33:57: #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 06:33:58: #1 tags after filtering in treatment: 34994199 INFO @ Fri, 05 Jul 2019 06:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:33:58: #1 finished! INFO @ Fri, 05 Jul 2019 06:33:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:34:04: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:34:04: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:34:04: #1 total tags in treatment: 34994397 INFO @ Fri, 05 Jul 2019 06:34:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:34:04: #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 06:34:04: #1 tags after filtering in treatment: 34994199 INFO @ Fri, 05 Jul 2019 06:34:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:34:04: #1 finished! INFO @ Fri, 05 Jul 2019 06:34:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:34:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:34:07: #2 number of paired peaks: 66038 INFO @ Fri, 05 Jul 2019 06:34:07: start model_add_line... INFO @ Fri, 05 Jul 2019 06:34:08: start X-correlation... INFO @ Fri, 05 Jul 2019 06:34:08: end of X-cor INFO @ Fri, 05 Jul 2019 06:34:08: #2 finished! INFO @ Fri, 05 Jul 2019 06:34:08: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:34:08: #2 alternative fragment length(s) may be 4,134 bps INFO @ Fri, 05 Jul 2019 06:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.20_model.r INFO @ Fri, 05 Jul 2019 06:34:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:34:13: #2 number of paired peaks: 66038 INFO @ Fri, 05 Jul 2019 06:34:13: start model_add_line... INFO @ Fri, 05 Jul 2019 06:34:14: start X-correlation... INFO @ Fri, 05 Jul 2019 06:34:14: end of X-cor INFO @ Fri, 05 Jul 2019 06:34:14: #2 finished! INFO @ Fri, 05 Jul 2019 06:34:14: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 06:34:14: #2 alternative fragment length(s) may be 4,134 bps INFO @ Fri, 05 Jul 2019 06:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.10_model.r INFO @ Fri, 05 Jul 2019 06:34:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:35:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:36:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:36:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.05_summits.bed INFO @ Fri, 05 Jul 2019 06:37:02: Done! pass1 - making usageList (163 chroms): 29 millis pass2 - checking and writing primary data (57663 records, 4 fields): 125 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:37:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:37:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:37:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.20_summits.bed INFO @ Fri, 05 Jul 2019 06:37:22: Done! pass1 - making usageList (114 chroms): 16 millis pass2 - checking and writing primary data (35294 records, 4 fields): 116 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:37:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:37:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101861/ERX101861.10_summits.bed INFO @ Fri, 05 Jul 2019 06:37:37: Done! pass1 - making usageList (143 chroms): 10 millis pass2 - checking and writing primary data (46681 records, 4 fields): 69 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。