Job ID = 4288858 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:22:31 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 ) 2019-12-10T03:23:25 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 ) 2019-12-10T03:27:25 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:33:04 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:40:40 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 : 48,180,731 reads read : 96,361,462 reads written : 48,180,731 reads 0-length : 48,180,731 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: 00:00:01 Multiseed full-index search: 00:42:59 48180731 reads; of these: 48180731 (100.00%) were unpaired; of these: 2279101 (4.73%) aligned 0 times 34235103 (71.06%) aligned exactly 1 time 11666527 (24.21%) aligned >1 times 95.27% overall alignment rate Time searching: 00:43:01 Overall time: 00:43:01 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 20 files... [bam_rmdupse_core] 8528622 / 45901630 = 0.1858 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:37:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.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 @ Tue, 10 Dec 2019 13:37:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:37:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:37:18: 1000000 INFO @ Tue, 10 Dec 2019 13:37:25: 2000000 INFO @ Tue, 10 Dec 2019 13:37:32: 3000000 INFO @ Tue, 10 Dec 2019 13:37:40: 4000000 INFO @ Tue, 10 Dec 2019 13:37:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.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 @ Tue, 10 Dec 2019 13:37:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:37:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:37:48: 5000000 INFO @ Tue, 10 Dec 2019 13:37:49: 1000000 INFO @ Tue, 10 Dec 2019 13:37:55: 6000000 INFO @ Tue, 10 Dec 2019 13:37:58: 2000000 INFO @ Tue, 10 Dec 2019 13:38:03: 7000000 INFO @ Tue, 10 Dec 2019 13:38:07: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:38:10: 8000000 INFO @ Tue, 10 Dec 2019 13:38:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.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 @ Tue, 10 Dec 2019 13:38:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:38:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:38:15: 4000000 INFO @ Tue, 10 Dec 2019 13:38:18: 9000000 INFO @ Tue, 10 Dec 2019 13:38:18: 1000000 INFO @ Tue, 10 Dec 2019 13:38:24: 5000000 INFO @ Tue, 10 Dec 2019 13:38:25: 10000000 INFO @ Tue, 10 Dec 2019 13:38:25: 2000000 INFO @ Tue, 10 Dec 2019 13:38:33: 3000000 INFO @ Tue, 10 Dec 2019 13:38:33: 6000000 INFO @ Tue, 10 Dec 2019 13:38:33: 11000000 INFO @ Tue, 10 Dec 2019 13:38:40: 4000000 INFO @ Tue, 10 Dec 2019 13:38:41: 12000000 INFO @ Tue, 10 Dec 2019 13:38:42: 7000000 INFO @ Tue, 10 Dec 2019 13:38:48: 13000000 INFO @ Tue, 10 Dec 2019 13:38:49: 5000000 INFO @ Tue, 10 Dec 2019 13:38:51: 8000000 INFO @ Tue, 10 Dec 2019 13:38:56: 14000000 INFO @ Tue, 10 Dec 2019 13:38:56: 6000000 INFO @ Tue, 10 Dec 2019 13:38:59: 9000000 INFO @ Tue, 10 Dec 2019 13:39:04: 15000000 INFO @ Tue, 10 Dec 2019 13:39:05: 7000000 INFO @ Tue, 10 Dec 2019 13:39:07: 10000000 INFO @ Tue, 10 Dec 2019 13:39:12: 8000000 INFO @ Tue, 10 Dec 2019 13:39:13: 16000000 INFO @ Tue, 10 Dec 2019 13:39:16: 11000000 INFO @ Tue, 10 Dec 2019 13:39:20: 9000000 INFO @ Tue, 10 Dec 2019 13:39:22: 17000000 INFO @ Tue, 10 Dec 2019 13:39:24: 12000000 INFO @ Tue, 10 Dec 2019 13:39:28: 10000000 INFO @ Tue, 10 Dec 2019 13:39:31: 18000000 INFO @ Tue, 10 Dec 2019 13:39:32: 13000000 INFO @ Tue, 10 Dec 2019 13:39:35: 11000000 INFO @ Tue, 10 Dec 2019 13:39:40: 14000000 INFO @ Tue, 10 Dec 2019 13:39:40: 19000000 INFO @ Tue, 10 Dec 2019 13:39:42: 12000000 INFO @ Tue, 10 Dec 2019 13:39:48: 15000000 INFO @ Tue, 10 Dec 2019 13:39:49: 13000000 INFO @ Tue, 10 Dec 2019 13:39:50: 20000000 INFO @ Tue, 10 Dec 2019 13:39:56: 16000000 INFO @ Tue, 10 Dec 2019 13:39:57: 14000000 INFO @ Tue, 10 Dec 2019 13:39:59: 21000000 INFO @ Tue, 10 Dec 2019 13:40:04: 15000000 INFO @ Tue, 10 Dec 2019 13:40:04: 17000000 INFO @ Tue, 10 Dec 2019 13:40:09: 22000000 INFO @ Tue, 10 Dec 2019 13:40:11: 16000000 INFO @ Tue, 10 Dec 2019 13:40:12: 18000000 INFO @ Tue, 10 Dec 2019 13:40:18: 23000000 INFO @ Tue, 10 Dec 2019 13:40:18: 17000000 INFO @ Tue, 10 Dec 2019 13:40:20: 19000000 INFO @ Tue, 10 Dec 2019 13:40:26: 18000000 INFO @ Tue, 10 Dec 2019 13:40:28: 24000000 INFO @ Tue, 10 Dec 2019 13:40:28: 20000000 INFO @ Tue, 10 Dec 2019 13:40:33: 19000000 INFO @ Tue, 10 Dec 2019 13:40:36: 21000000 INFO @ Tue, 10 Dec 2019 13:40:37: 25000000 INFO @ Tue, 10 Dec 2019 13:40:40: 20000000 INFO @ Tue, 10 Dec 2019 13:40:44: 22000000 INFO @ Tue, 10 Dec 2019 13:40:47: 26000000 INFO @ Tue, 10 Dec 2019 13:40:47: 21000000 INFO @ Tue, 10 Dec 2019 13:40:51: 23000000 INFO @ Tue, 10 Dec 2019 13:40:54: 22000000 INFO @ Tue, 10 Dec 2019 13:40:57: 27000000 INFO @ Tue, 10 Dec 2019 13:40:59: 24000000 INFO @ Tue, 10 Dec 2019 13:41:01: 23000000 INFO @ Tue, 10 Dec 2019 13:41:06: 28000000 INFO @ Tue, 10 Dec 2019 13:41:07: 25000000 INFO @ Tue, 10 Dec 2019 13:41:08: 24000000 INFO @ Tue, 10 Dec 2019 13:41:15: 26000000 INFO @ Tue, 10 Dec 2019 13:41:15: 25000000 INFO @ Tue, 10 Dec 2019 13:41:16: 29000000 INFO @ Tue, 10 Dec 2019 13:41:23: 26000000 INFO @ Tue, 10 Dec 2019 13:41:23: 27000000 INFO @ Tue, 10 Dec 2019 13:41:26: 30000000 INFO @ Tue, 10 Dec 2019 13:41:30: 27000000 INFO @ Tue, 10 Dec 2019 13:41:31: 28000000 INFO @ Tue, 10 Dec 2019 13:41:36: 31000000 INFO @ Tue, 10 Dec 2019 13:41:38: 28000000 INFO @ Tue, 10 Dec 2019 13:41:39: 29000000 INFO @ Tue, 10 Dec 2019 13:41:45: 29000000 INFO @ Tue, 10 Dec 2019 13:41:46: 32000000 INFO @ Tue, 10 Dec 2019 13:41:48: 30000000 INFO @ Tue, 10 Dec 2019 13:41:52: 30000000 INFO @ Tue, 10 Dec 2019 13:41:56: 31000000 INFO @ Tue, 10 Dec 2019 13:41:56: 33000000 INFO @ Tue, 10 Dec 2019 13:41:59: 31000000 INFO @ Tue, 10 Dec 2019 13:42:04: 32000000 INFO @ Tue, 10 Dec 2019 13:42:06: 34000000 INFO @ Tue, 10 Dec 2019 13:42:07: 32000000 INFO @ Tue, 10 Dec 2019 13:42:12: 33000000 INFO @ Tue, 10 Dec 2019 13:42:15: 33000000 INFO @ Tue, 10 Dec 2019 13:42:16: 35000000 INFO @ Tue, 10 Dec 2019 13:42:20: 34000000 INFO @ Tue, 10 Dec 2019 13:42:23: 34000000 INFO @ Tue, 10 Dec 2019 13:42:27: 36000000 INFO @ Tue, 10 Dec 2019 13:42:28: 35000000 INFO @ Tue, 10 Dec 2019 13:42:31: 35000000 INFO @ Tue, 10 Dec 2019 13:42:37: 37000000 INFO @ Tue, 10 Dec 2019 13:42:37: 36000000 INFO @ Tue, 10 Dec 2019 13:42:39: 36000000 INFO @ Tue, 10 Dec 2019 13:42:40: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:42:40: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:42:40: #1 total tags in treatment: 37373008 INFO @ Tue, 10 Dec 2019 13:42:40: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:42:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:42:41: #1 tags after filtering in treatment: 37372888 INFO @ Tue, 10 Dec 2019 13:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:42:41: #1 finished! INFO @ Tue, 10 Dec 2019 13:42:41: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:42:46: 37000000 INFO @ Tue, 10 Dec 2019 13:42:47: 37000000 INFO @ Tue, 10 Dec 2019 13:42:48: #2 number of paired peaks: 60394 INFO @ Tue, 10 Dec 2019 13:42:48: start model_add_line... INFO @ Tue, 10 Dec 2019 13:42:49: start X-correlation... INFO @ Tue, 10 Dec 2019 13:42:49: end of X-cor INFO @ Tue, 10 Dec 2019 13:42:49: #2 finished! INFO @ Tue, 10 Dec 2019 13:42:49: #2 predicted fragment length is 151 bps INFO @ Tue, 10 Dec 2019 13:42:49: #2 alternative fragment length(s) may be 2,151 bps INFO @ Tue, 10 Dec 2019 13:42:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.05_model.r INFO @ Tue, 10 Dec 2019 13:42:49: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:42:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:42:49: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:42:49: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:42:49: #1 total tags in treatment: 37373008 INFO @ Tue, 10 Dec 2019 13:42:49: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:42:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:42:50: #1 tags after filtering in treatment: 37372888 INFO @ Tue, 10 Dec 2019 13:42:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:42:50: #1 finished! INFO @ Tue, 10 Dec 2019 13:42:50: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:42:50: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:42:50: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:42:50: #1 total tags in treatment: 37373008 INFO @ Tue, 10 Dec 2019 13:42:50: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:42:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:42:51: #1 tags after filtering in treatment: 37372888 INFO @ Tue, 10 Dec 2019 13:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:42:51: #1 finished! INFO @ Tue, 10 Dec 2019 13:42:51: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:42:57: #2 number of paired peaks: 60394 INFO @ Tue, 10 Dec 2019 13:42:57: start model_add_line... INFO @ Tue, 10 Dec 2019 13:42:57: start X-correlation... INFO @ Tue, 10 Dec 2019 13:42:57: end of X-cor INFO @ Tue, 10 Dec 2019 13:42:57: #2 finished! INFO @ Tue, 10 Dec 2019 13:42:57: #2 predicted fragment length is 151 bps INFO @ Tue, 10 Dec 2019 13:42:57: #2 alternative fragment length(s) may be 2,151 bps INFO @ Tue, 10 Dec 2019 13:42:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.10_model.r INFO @ Tue, 10 Dec 2019 13:42:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:42:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:42:58: #2 number of paired peaks: 60394 INFO @ Tue, 10 Dec 2019 13:42:58: start model_add_line... INFO @ Tue, 10 Dec 2019 13:42:58: start X-correlation... INFO @ Tue, 10 Dec 2019 13:42:58: end of X-cor INFO @ Tue, 10 Dec 2019 13:42:58: #2 finished! INFO @ Tue, 10 Dec 2019 13:42:58: #2 predicted fragment length is 151 bps INFO @ Tue, 10 Dec 2019 13:42:58: #2 alternative fragment length(s) may be 2,151 bps INFO @ Tue, 10 Dec 2019 13:42:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.20_model.r INFO @ Tue, 10 Dec 2019 13:42:58: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:44:48: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:44:58: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:44:58: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:45:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:45:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:45:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.05_summits.bed INFO @ Tue, 10 Dec 2019 13:45:50: Done! pass1 - making usageList (117 chroms): 8 millis pass2 - checking and writing primary data (16034 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.10_summits.bed INFO @ Tue, 10 Dec 2019 13:45:59: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (2501 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779822/SRX4779822.20_summits.bed INFO @ Tue, 10 Dec 2019 13:45:59: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (350 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。