Job ID = 2003681 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T04:15:03 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 ) 2019-07-05T04:15:37 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T04:15:37 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.45' 2019-07-05T04:15:37 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.24) from '172.19.7.45' spots read : 35,742,942 reads read : 35,742,942 reads written : 35,742,942 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: 00:00:07 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:31 35742942 reads; of these: 35742942 (100.00%) were unpaired; of these: 2937107 (8.22%) aligned 0 times 23036832 (64.45%) aligned exactly 1 time 9769003 (27.33%) aligned >1 times 91.78% overall alignment rate Time searching: 00:27:40 Overall time: 00:27:40 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 16 files... [bam_rmdupse_core] 2056263 / 32805835 = 0.0627 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 14:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.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 14:34:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:34:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.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 14:34:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:34:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.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 14:34:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:34:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:34:21: 1000000 INFO @ Fri, 05 Jul 2019 14:34:21: 1000000 INFO @ Fri, 05 Jul 2019 14:34:22: 1000000 INFO @ Fri, 05 Jul 2019 14:34:28: 2000000 INFO @ Fri, 05 Jul 2019 14:34:30: 2000000 INFO @ Fri, 05 Jul 2019 14:34:31: 2000000 INFO @ Fri, 05 Jul 2019 14:34:35: 3000000 INFO @ Fri, 05 Jul 2019 14:34:38: 3000000 INFO @ Fri, 05 Jul 2019 14:34:39: 3000000 INFO @ Fri, 05 Jul 2019 14:34:43: 4000000 INFO @ Fri, 05 Jul 2019 14:34:46: 4000000 INFO @ Fri, 05 Jul 2019 14:34:50: 4000000 INFO @ Fri, 05 Jul 2019 14:34:50: 5000000 INFO @ Fri, 05 Jul 2019 14:34:54: 5000000 INFO @ Fri, 05 Jul 2019 14:34:57: 6000000 INFO @ Fri, 05 Jul 2019 14:34:58: 5000000 INFO @ Fri, 05 Jul 2019 14:35:03: 6000000 INFO @ Fri, 05 Jul 2019 14:35:05: 7000000 INFO @ Fri, 05 Jul 2019 14:35:06: 6000000 INFO @ Fri, 05 Jul 2019 14:35:11: 7000000 INFO @ Fri, 05 Jul 2019 14:35:12: 8000000 INFO @ Fri, 05 Jul 2019 14:35:15: 7000000 INFO @ Fri, 05 Jul 2019 14:35:19: 9000000 INFO @ Fri, 05 Jul 2019 14:35:19: 8000000 INFO @ Fri, 05 Jul 2019 14:35:24: 8000000 INFO @ Fri, 05 Jul 2019 14:35:27: 10000000 INFO @ Fri, 05 Jul 2019 14:35:28: 9000000 INFO @ Fri, 05 Jul 2019 14:35:33: 9000000 INFO @ Fri, 05 Jul 2019 14:35:34: 11000000 INFO @ Fri, 05 Jul 2019 14:35:36: 10000000 INFO @ Fri, 05 Jul 2019 14:35:41: 12000000 INFO @ Fri, 05 Jul 2019 14:35:42: 10000000 INFO @ Fri, 05 Jul 2019 14:35:45: 11000000 INFO @ Fri, 05 Jul 2019 14:35:48: 13000000 INFO @ Fri, 05 Jul 2019 14:35:51: 11000000 INFO @ Fri, 05 Jul 2019 14:35:54: 12000000 INFO @ Fri, 05 Jul 2019 14:35:56: 14000000 INFO @ Fri, 05 Jul 2019 14:36:00: 12000000 INFO @ Fri, 05 Jul 2019 14:36:02: 13000000 INFO @ Fri, 05 Jul 2019 14:36:03: 15000000 INFO @ Fri, 05 Jul 2019 14:36:10: 13000000 INFO @ Fri, 05 Jul 2019 14:36:10: 16000000 INFO @ Fri, 05 Jul 2019 14:36:11: 14000000 INFO @ Fri, 05 Jul 2019 14:36:17: 17000000 INFO @ Fri, 05 Jul 2019 14:36:19: 14000000 INFO @ Fri, 05 Jul 2019 14:36:19: 15000000 INFO @ Fri, 05 Jul 2019 14:36:25: 18000000 INFO @ Fri, 05 Jul 2019 14:36:27: 16000000 INFO @ Fri, 05 Jul 2019 14:36:28: 15000000 INFO @ Fri, 05 Jul 2019 14:36:33: 19000000 INFO @ Fri, 05 Jul 2019 14:36:36: 17000000 INFO @ Fri, 05 Jul 2019 14:36:37: 16000000 INFO @ Fri, 05 Jul 2019 14:36:40: 20000000 INFO @ Fri, 05 Jul 2019 14:36:44: 18000000 INFO @ Fri, 05 Jul 2019 14:36:46: 17000000 INFO @ Fri, 05 Jul 2019 14:36:48: 21000000 INFO @ Fri, 05 Jul 2019 14:36:53: 19000000 INFO @ Fri, 05 Jul 2019 14:36:55: 22000000 INFO @ Fri, 05 Jul 2019 14:36:55: 18000000 INFO @ Fri, 05 Jul 2019 14:37:01: 20000000 INFO @ Fri, 05 Jul 2019 14:37:02: 23000000 INFO @ Fri, 05 Jul 2019 14:37:04: 19000000 INFO @ Fri, 05 Jul 2019 14:37:09: 21000000 INFO @ Fri, 05 Jul 2019 14:37:10: 24000000 INFO @ Fri, 05 Jul 2019 14:37:13: 20000000 INFO @ Fri, 05 Jul 2019 14:37:17: 25000000 INFO @ Fri, 05 Jul 2019 14:37:18: 22000000 INFO @ Fri, 05 Jul 2019 14:37:22: 21000000 INFO @ Fri, 05 Jul 2019 14:37:25: 26000000 INFO @ Fri, 05 Jul 2019 14:37:27: 23000000 INFO @ Fri, 05 Jul 2019 14:37:32: 22000000 INFO @ Fri, 05 Jul 2019 14:37:32: 27000000 INFO @ Fri, 05 Jul 2019 14:37:36: 24000000 INFO @ Fri, 05 Jul 2019 14:37:40: 28000000 INFO @ Fri, 05 Jul 2019 14:37:42: 23000000 INFO @ Fri, 05 Jul 2019 14:37:45: 25000000 INFO @ Fri, 05 Jul 2019 14:37:47: 29000000 INFO @ Fri, 05 Jul 2019 14:37:52: 24000000 INFO @ Fri, 05 Jul 2019 14:37:53: 26000000 INFO @ Fri, 05 Jul 2019 14:37:55: 30000000 INFO @ Fri, 05 Jul 2019 14:38:01: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:38:01: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:38:01: #1 total tags in treatment: 30749572 INFO @ Fri, 05 Jul 2019 14:38:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:38:01: #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 14:38:01: #1 tags after filtering in treatment: 30749479 INFO @ Fri, 05 Jul 2019 14:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:38:01: #1 finished! INFO @ Fri, 05 Jul 2019 14:38:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:38:01: 25000000 INFO @ Fri, 05 Jul 2019 14:38:02: 27000000 INFO @ Fri, 05 Jul 2019 14:38:05: #2 number of paired peaks: 9090 INFO @ Fri, 05 Jul 2019 14:38:05: start model_add_line... INFO @ Fri, 05 Jul 2019 14:38:05: start X-correlation... INFO @ Fri, 05 Jul 2019 14:38:05: end of X-cor INFO @ Fri, 05 Jul 2019 14:38:05: #2 finished! INFO @ Fri, 05 Jul 2019 14:38:05: #2 predicted fragment length is 114 bps INFO @ Fri, 05 Jul 2019 14:38:05: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 05 Jul 2019 14:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.10_model.r INFO @ Fri, 05 Jul 2019 14:38:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:38:11: 28000000 INFO @ Fri, 05 Jul 2019 14:38:11: 26000000 INFO @ Fri, 05 Jul 2019 14:38:19: 29000000 INFO @ Fri, 05 Jul 2019 14:38:21: 27000000 INFO @ Fri, 05 Jul 2019 14:38:28: 30000000 INFO @ Fri, 05 Jul 2019 14:38:30: 28000000 INFO @ Fri, 05 Jul 2019 14:38:35: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:38:35: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:38:35: #1 total tags in treatment: 30749572 INFO @ Fri, 05 Jul 2019 14:38:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:38:35: #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 14:38:35: #1 tags after filtering in treatment: 30749479 INFO @ Fri, 05 Jul 2019 14:38:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:38:35: #1 finished! INFO @ Fri, 05 Jul 2019 14:38:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:38:39: #2 number of paired peaks: 9090 INFO @ Fri, 05 Jul 2019 14:38:39: start model_add_line... INFO @ Fri, 05 Jul 2019 14:38:39: 29000000 INFO @ Fri, 05 Jul 2019 14:38:39: start X-correlation... INFO @ Fri, 05 Jul 2019 14:38:39: end of X-cor INFO @ Fri, 05 Jul 2019 14:38:39: #2 finished! INFO @ Fri, 05 Jul 2019 14:38:39: #2 predicted fragment length is 114 bps INFO @ Fri, 05 Jul 2019 14:38:39: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 05 Jul 2019 14:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.05_model.r INFO @ Fri, 05 Jul 2019 14:38:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:38:50: 30000000 INFO @ Fri, 05 Jul 2019 14:38:57: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:38:57: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:38:57: #1 total tags in treatment: 30749572 INFO @ Fri, 05 Jul 2019 14:38:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:38:57: #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 14:38:58: #1 tags after filtering in treatment: 30749479 INFO @ Fri, 05 Jul 2019 14:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:38:58: #1 finished! INFO @ Fri, 05 Jul 2019 14:38:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:39:02: #2 number of paired peaks: 9090 INFO @ Fri, 05 Jul 2019 14:39:02: start model_add_line... INFO @ Fri, 05 Jul 2019 14:39:02: start X-correlation... INFO @ Fri, 05 Jul 2019 14:39:02: end of X-cor INFO @ Fri, 05 Jul 2019 14:39:02: #2 finished! INFO @ Fri, 05 Jul 2019 14:39:02: #2 predicted fragment length is 114 bps INFO @ Fri, 05 Jul 2019 14:39:02: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 05 Jul 2019 14:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.20_model.r INFO @ Fri, 05 Jul 2019 14:39:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:39:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:39:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:40:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.10_summits.bed INFO @ Fri, 05 Jul 2019 14:40:34: Done! pass1 - making usageList (46 chroms): 3 millis pass2 - checking and writing primary data (3344 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:40:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:41:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:41:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:41:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.05_summits.bed INFO @ Fri, 05 Jul 2019 14:41:07: Done! pass1 - making usageList (60 chroms): 4 millis pass2 - checking and writing primary data (6059 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:41:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:41:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:41:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423105/SRX423105.20_summits.bed INFO @ Fri, 05 Jul 2019 14:41:28: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (1347 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。