Job ID = 2001674 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T23:07:48 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 ) 2019-07-04T23:09:06 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 ) 2019-07-04T23:10:17 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 ) spots read : 24,115,941 reads read : 24,115,941 reads written : 24,115,941 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: 00:00:01 Multiseed full-index search: 00:09:02 24115941 reads; of these: 24115941 (100.00%) were unpaired; of these: 666555 (2.76%) aligned 0 times 17641424 (73.15%) aligned exactly 1 time 5807962 (24.08%) aligned >1 times 97.24% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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 8 files... [bam_rmdupse_core] 1582963 / 23449386 = 0.0675 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 08:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.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 08:28:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:28:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.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 08:29:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:29:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.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 08:29:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:29:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:29:08: 1000000 INFO @ Fri, 05 Jul 2019 08:29:09: 1000000 INFO @ Fri, 05 Jul 2019 08:29:11: 1000000 INFO @ Fri, 05 Jul 2019 08:29:16: 2000000 INFO @ Fri, 05 Jul 2019 08:29:17: 2000000 INFO @ Fri, 05 Jul 2019 08:29:18: 2000000 INFO @ Fri, 05 Jul 2019 08:29:24: 3000000 INFO @ Fri, 05 Jul 2019 08:29:25: 3000000 INFO @ Fri, 05 Jul 2019 08:29:26: 3000000 INFO @ Fri, 05 Jul 2019 08:29:32: 4000000 INFO @ Fri, 05 Jul 2019 08:29:34: 4000000 INFO @ Fri, 05 Jul 2019 08:29:34: 4000000 INFO @ Fri, 05 Jul 2019 08:29:40: 5000000 INFO @ Fri, 05 Jul 2019 08:29:42: 5000000 INFO @ Fri, 05 Jul 2019 08:29:44: 5000000 INFO @ Fri, 05 Jul 2019 08:29:48: 6000000 INFO @ Fri, 05 Jul 2019 08:29:49: 6000000 INFO @ Fri, 05 Jul 2019 08:29:52: 6000000 INFO @ Fri, 05 Jul 2019 08:29:56: 7000000 INFO @ Fri, 05 Jul 2019 08:29:57: 7000000 INFO @ Fri, 05 Jul 2019 08:30:01: 7000000 INFO @ Fri, 05 Jul 2019 08:30:04: 8000000 INFO @ Fri, 05 Jul 2019 08:30:06: 8000000 INFO @ Fri, 05 Jul 2019 08:30:10: 8000000 INFO @ Fri, 05 Jul 2019 08:30:12: 9000000 INFO @ Fri, 05 Jul 2019 08:30:14: 9000000 INFO @ Fri, 05 Jul 2019 08:30:18: 9000000 INFO @ Fri, 05 Jul 2019 08:30:20: 10000000 INFO @ Fri, 05 Jul 2019 08:30:22: 10000000 INFO @ Fri, 05 Jul 2019 08:30:27: 10000000 INFO @ Fri, 05 Jul 2019 08:30:28: 11000000 INFO @ Fri, 05 Jul 2019 08:30:30: 11000000 INFO @ Fri, 05 Jul 2019 08:30:36: 12000000 INFO @ Fri, 05 Jul 2019 08:30:36: 11000000 INFO @ Fri, 05 Jul 2019 08:30:38: 12000000 INFO @ Fri, 05 Jul 2019 08:30:44: 13000000 INFO @ Fri, 05 Jul 2019 08:30:45: 12000000 INFO @ Fri, 05 Jul 2019 08:30:46: 13000000 INFO @ Fri, 05 Jul 2019 08:30:52: 14000000 INFO @ Fri, 05 Jul 2019 08:30:54: 13000000 INFO @ Fri, 05 Jul 2019 08:30:54: 14000000 INFO @ Fri, 05 Jul 2019 08:31:00: 15000000 INFO @ Fri, 05 Jul 2019 08:31:02: 15000000 INFO @ Fri, 05 Jul 2019 08:31:03: 14000000 INFO @ Fri, 05 Jul 2019 08:31:08: 16000000 INFO @ Fri, 05 Jul 2019 08:31:11: 16000000 INFO @ Fri, 05 Jul 2019 08:31:12: 15000000 INFO @ Fri, 05 Jul 2019 08:31:17: 17000000 INFO @ Fri, 05 Jul 2019 08:31:19: 17000000 INFO @ Fri, 05 Jul 2019 08:31:21: 16000000 INFO @ Fri, 05 Jul 2019 08:31:25: 18000000 INFO @ Fri, 05 Jul 2019 08:31:28: 18000000 INFO @ Fri, 05 Jul 2019 08:31:30: 17000000 INFO @ Fri, 05 Jul 2019 08:31:33: 19000000 INFO @ Fri, 05 Jul 2019 08:31:36: 19000000 INFO @ Fri, 05 Jul 2019 08:31:39: 18000000 INFO @ Fri, 05 Jul 2019 08:31:41: 20000000 INFO @ Fri, 05 Jul 2019 08:31:45: 20000000 INFO @ Fri, 05 Jul 2019 08:31:48: 19000000 INFO @ Fri, 05 Jul 2019 08:31:50: 21000000 INFO @ Fri, 05 Jul 2019 08:31:54: 21000000 INFO @ Fri, 05 Jul 2019 08:31:57: 20000000 INFO @ Fri, 05 Jul 2019 08:31:57: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:31:57: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:31:57: #1 total tags in treatment: 21866423 INFO @ Fri, 05 Jul 2019 08:31:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:31:57: #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 08:31:58: #1 tags after filtering in treatment: 21866255 INFO @ Fri, 05 Jul 2019 08:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:31:58: #1 finished! INFO @ Fri, 05 Jul 2019 08:31:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:32:01: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:32:01: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:32:01: #1 total tags in treatment: 21866423 INFO @ Fri, 05 Jul 2019 08:32:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:32:01: #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 08:32:02: #1 tags after filtering in treatment: 21866255 INFO @ Fri, 05 Jul 2019 08:32:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:32:02: #1 finished! INFO @ Fri, 05 Jul 2019 08:32:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:32:03: #2 number of paired peaks: 57909 INFO @ Fri, 05 Jul 2019 08:32:03: start model_add_line... INFO @ Fri, 05 Jul 2019 08:32:03: start X-correlation... INFO @ Fri, 05 Jul 2019 08:32:03: end of X-cor INFO @ Fri, 05 Jul 2019 08:32:03: #2 finished! INFO @ Fri, 05 Jul 2019 08:32:03: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 08:32:03: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 08:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.05_model.r INFO @ Fri, 05 Jul 2019 08:32:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:32:05: 21000000 INFO @ Fri, 05 Jul 2019 08:32:06: #2 number of paired peaks: 57909 INFO @ Fri, 05 Jul 2019 08:32:06: start model_add_line... INFO @ Fri, 05 Jul 2019 08:32:07: start X-correlation... INFO @ Fri, 05 Jul 2019 08:32:07: end of X-cor INFO @ Fri, 05 Jul 2019 08:32:07: #2 finished! INFO @ Fri, 05 Jul 2019 08:32:07: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 08:32:07: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 08:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.10_model.r INFO @ Fri, 05 Jul 2019 08:32:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:32:13: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:32:13: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:32:13: #1 total tags in treatment: 21866423 INFO @ Fri, 05 Jul 2019 08:32:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:32:13: #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 08:32:14: #1 tags after filtering in treatment: 21866255 INFO @ Fri, 05 Jul 2019 08:32:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:32:14: #1 finished! INFO @ Fri, 05 Jul 2019 08:32:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:32:18: #2 number of paired peaks: 57909 INFO @ Fri, 05 Jul 2019 08:32:18: start model_add_line... INFO @ Fri, 05 Jul 2019 08:32:19: start X-correlation... INFO @ Fri, 05 Jul 2019 08:32:19: end of X-cor INFO @ Fri, 05 Jul 2019 08:32:19: #2 finished! INFO @ Fri, 05 Jul 2019 08:32:19: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 08:32:19: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 08:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.20_model.r INFO @ Fri, 05 Jul 2019 08:32:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:33:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:33:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:33:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:33:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:33:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:33:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.05_summits.bed INFO @ Fri, 05 Jul 2019 08:33:50: Done! pass1 - making usageList (64 chroms): 3 millis pass2 - checking and writing primary data (5728 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:33:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:33:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:33:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.10_summits.bed INFO @ Fri, 05 Jul 2019 08:33:53: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1338 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101989/ERX101989.20_summits.bed INFO @ Fri, 05 Jul 2019 08:34:02: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (142 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。