Job ID = 2640456 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:55:50 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 ) 2019-08-24T07:55:50 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 ) 2019-08-24T07:55:50 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 ) 2019-08-24T07:55:50 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 ) 2019-08-24T07:58:14 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 ) 2019-08-24T07:58:14 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 ) 2019-08-24T07:59:14 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 ) 2019-08-24T08:03:31 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 ) 2019-08-24T08:07:47 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 ) 2019-08-24T08:08:55 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:12:18 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 ) 2019-08-24T08:13:28 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 ) 2019-08-24T08:27:17 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 ) 2019-08-24T08:27:50 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 ) 2019-08-24T08:31:49 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 ) 2019-08-24T08:34:56 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 ) 2019-08-24T08:40:27 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 ) 2019-08-24T08:40:27 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 ) 2019-08-24T08:40:58 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 ) 2019-08-24T08:43:17 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 ) 2019-08-24T08:43:17 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 ) 2019-08-24T08:44:43 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 ) 2019-08-24T08:44:43 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 ) 2019-08-24T08:45:27 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 ) 2019-08-24T08:47:03 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 ) 2019-08-24T08:47:03 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 ) 2019-08-24T09:12:05 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 ) spots read : 414,775,139 reads read : 829,550,278 reads written : 414,775,139 reads 0-length : 414,775,139 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: 00:00:02 Time loading forward index: 00:00:06 Time loading mirror index: 00:00:03 Multiseed full-index search: 01:27:23 414775139 reads; of these: 414775139 (100.00%) were unpaired; of these: 348426154 (84.00%) aligned 0 times 40599961 (9.79%) aligned exactly 1 time 25749024 (6.21%) aligned >1 times 16.00% overall alignment rate Time searching: 01:27:34 Overall time: 01:27:34 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] 57900689 / 66348985 = 0.8727 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.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 20:13:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:13:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:14:05: 1000000 INFO @ Sat, 24 Aug 2019 20:14:13: 2000000 INFO @ Sat, 24 Aug 2019 20:14:21: 3000000 INFO @ Sat, 24 Aug 2019 20:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.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 20:14:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:14:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:14:29: 4000000 INFO @ Sat, 24 Aug 2019 20:14:34: 1000000 INFO @ Sat, 24 Aug 2019 20:14:38: 5000000 INFO @ Sat, 24 Aug 2019 20:14:43: 2000000 INFO @ Sat, 24 Aug 2019 20:14:46: 6000000 INFO @ Sat, 24 Aug 2019 20:14:52: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:14:55: 7000000 INFO @ Sat, 24 Aug 2019 20:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.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 20:14:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:14:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:15:00: 4000000 INFO @ Sat, 24 Aug 2019 20:15:03: 1000000 INFO @ Sat, 24 Aug 2019 20:15:04: 8000000 INFO @ Sat, 24 Aug 2019 20:15:07: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 20:15:07: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 20:15:07: #1 total tags in treatment: 8448296 INFO @ Sat, 24 Aug 2019 20:15:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:15:07: #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 20:15:08: #1 tags after filtering in treatment: 8448121 INFO @ Sat, 24 Aug 2019 20:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:15:08: #1 finished! INFO @ Sat, 24 Aug 2019 20:15:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:15:09: 5000000 INFO @ Sat, 24 Aug 2019 20:15:10: #2 number of paired peaks: 12574 INFO @ Sat, 24 Aug 2019 20:15:10: start model_add_line... INFO @ Sat, 24 Aug 2019 20:15:10: start X-correlation... INFO @ Sat, 24 Aug 2019 20:15:10: end of X-cor INFO @ Sat, 24 Aug 2019 20:15:10: #2 finished! INFO @ Sat, 24 Aug 2019 20:15:10: #2 predicted fragment length is 46 bps INFO @ Sat, 24 Aug 2019 20:15:10: #2 alternative fragment length(s) may be 46,590 bps INFO @ Sat, 24 Aug 2019 20:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.05_model.r WARNING @ Sat, 24 Aug 2019 20:15:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 20:15:10: #2 You may need to consider one of the other alternative d(s): 46,590 WARNING @ Sat, 24 Aug 2019 20:15:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 20:15:10: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:15:11: 2000000 INFO @ Sat, 24 Aug 2019 20:15:17: 6000000 INFO @ Sat, 24 Aug 2019 20:15:18: 3000000 INFO @ Sat, 24 Aug 2019 20:15:25: 4000000 INFO @ Sat, 24 Aug 2019 20:15:26: 7000000 INFO @ Sat, 24 Aug 2019 20:15:32: 5000000 INFO @ Sat, 24 Aug 2019 20:15:34: 8000000 INFO @ Sat, 24 Aug 2019 20:15:37: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:15:38: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 20:15:38: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 20:15:38: #1 total tags in treatment: 8448296 INFO @ Sat, 24 Aug 2019 20:15:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:15:38: #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 20:15:39: #1 tags after filtering in treatment: 8448121 INFO @ Sat, 24 Aug 2019 20:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:15:39: #1 finished! INFO @ Sat, 24 Aug 2019 20:15:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:15:39: 6000000 INFO @ Sat, 24 Aug 2019 20:15:41: #2 number of paired peaks: 12574 INFO @ Sat, 24 Aug 2019 20:15:41: start model_add_line... INFO @ Sat, 24 Aug 2019 20:15:41: start X-correlation... INFO @ Sat, 24 Aug 2019 20:15:41: end of X-cor INFO @ Sat, 24 Aug 2019 20:15:41: #2 finished! INFO @ Sat, 24 Aug 2019 20:15:41: #2 predicted fragment length is 46 bps INFO @ Sat, 24 Aug 2019 20:15:41: #2 alternative fragment length(s) may be 46,590 bps INFO @ Sat, 24 Aug 2019 20:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.10_model.r WARNING @ Sat, 24 Aug 2019 20:15:41: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 20:15:41: #2 You may need to consider one of the other alternative d(s): 46,590 WARNING @ Sat, 24 Aug 2019 20:15:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 20:15:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:15:46: 7000000 INFO @ Sat, 24 Aug 2019 20:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.05_peaks.xls INFO @ Sat, 24 Aug 2019 20:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.05_summits.bed INFO @ Sat, 24 Aug 2019 20:15:49: Done! pass1 - making usageList (21 chroms): 2 millis pass2 - checking and writing primary data (343 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:15:53: 8000000 INFO @ Sat, 24 Aug 2019 20:15:56: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 20:15:56: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 20:15:56: #1 total tags in treatment: 8448296 INFO @ Sat, 24 Aug 2019 20:15:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:15:56: #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 20:15:57: #1 tags after filtering in treatment: 8448121 INFO @ Sat, 24 Aug 2019 20:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:15:57: #1 finished! INFO @ Sat, 24 Aug 2019 20:15:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:15:59: #2 number of paired peaks: 12574 INFO @ Sat, 24 Aug 2019 20:15:59: start model_add_line... INFO @ Sat, 24 Aug 2019 20:15:59: start X-correlation... INFO @ Sat, 24 Aug 2019 20:15:59: end of X-cor INFO @ Sat, 24 Aug 2019 20:15:59: #2 finished! INFO @ Sat, 24 Aug 2019 20:15:59: #2 predicted fragment length is 46 bps INFO @ Sat, 24 Aug 2019 20:15:59: #2 alternative fragment length(s) may be 46,590 bps INFO @ Sat, 24 Aug 2019 20:15:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.20_model.r WARNING @ Sat, 24 Aug 2019 20:15:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 20:15:59: #2 You may need to consider one of the other alternative d(s): 46,590 WARNING @ Sat, 24 Aug 2019 20:15:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 20:15:59: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:16:07: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:16:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.10_peaks.xls INFO @ Sat, 24 Aug 2019 20:16:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:16:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.10_summits.bed INFO @ Sat, 24 Aug 2019 20:16:20: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:16:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.20_peaks.xls INFO @ Sat, 24 Aug 2019 20:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094897/SRX5094897.20_summits.bed INFO @ Sat, 24 Aug 2019 20:16:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。