Job ID = 2640452 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:50:54 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 ) 2019-08-24T07:51:34 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 ) 2019-08-24T07:52:37 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 ) 2019-08-24T07:54:41 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 ) 2019-08-24T07:55:50 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 ) 2019-08-24T07:56:33 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 ) 2019-08-24T07:57:15 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 ) 2019-08-24T07:57:15 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 ) 2019-08-24T07:57:15 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 ) 2019-08-24T07:57:15 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 ) 2019-08-24T08:03:30 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 ) 2019-08-24T08:05:10 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 ) 2019-08-24T08:06:24 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 ) 2019-08-24T08:08:07 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 ) 2019-08-24T08:12:31 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 ) 2019-08-24T08:13:40 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 ) 2019-08-24T08:18:44 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 ) 2019-08-24T08:28:08 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 ) 2019-08-24T08:28:15 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 ) 2019-08-24T08:28:15 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 ) spots read : 411,270,916 reads read : 822,541,832 reads written : 411,270,916 reads 0-length : 411,270,916 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:15:58 411270916 reads; of these: 411270916 (100.00%) were unpaired; of these: 351612096 (85.49%) aligned 0 times 34125909 (8.30%) aligned exactly 1 time 25532911 (6.21%) aligned >1 times 14.51% overall alignment rate Time searching: 01:16:02 Overall time: 01:16:02 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] 50397266 / 59658820 = 0.8448 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.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 19:41:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:41:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:41:14: 1000000 INFO @ Sat, 24 Aug 2019 19:41:20: 2000000 INFO @ Sat, 24 Aug 2019 19:41:27: 3000000 INFO @ Sat, 24 Aug 2019 19:41:34: 4000000 INFO @ Sat, 24 Aug 2019 19:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.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 19:41:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:41:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:41:41: 5000000 INFO @ Sat, 24 Aug 2019 19:41:44: 1000000 INFO @ Sat, 24 Aug 2019 19:41:48: 6000000 INFO @ Sat, 24 Aug 2019 19:41:52: 2000000 INFO @ Sat, 24 Aug 2019 19:41:55: 7000000 INFO @ Sat, 24 Aug 2019 19:41:59: 3000000 INFO @ Sat, 24 Aug 2019 19:42:02: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.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 19:42:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:42:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:42:07: 4000000 INFO @ Sat, 24 Aug 2019 19:42:10: 9000000 INFO @ Sat, 24 Aug 2019 19:42:11: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:42:11: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:42:11: #1 total tags in treatment: 9261554 INFO @ Sat, 24 Aug 2019 19:42:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:42:11: #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 19:42:12: #1 tags after filtering in treatment: 9261407 INFO @ Sat, 24 Aug 2019 19:42:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:42:12: #1 finished! INFO @ Sat, 24 Aug 2019 19:42:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:42:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:42:14: 1000000 INFO @ Sat, 24 Aug 2019 19:42:14: #2 number of paired peaks: 12967 INFO @ Sat, 24 Aug 2019 19:42:14: start model_add_line... INFO @ Sat, 24 Aug 2019 19:42:14: start X-correlation... INFO @ Sat, 24 Aug 2019 19:42:14: end of X-cor INFO @ Sat, 24 Aug 2019 19:42:14: #2 finished! INFO @ Sat, 24 Aug 2019 19:42:14: #2 predicted fragment length is 46 bps INFO @ Sat, 24 Aug 2019 19:42:14: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 24 Aug 2019 19:42:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.05_model.r WARNING @ Sat, 24 Aug 2019 19:42:14: #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 19:42:14: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 24 Aug 2019 19:42:14: #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 19:42:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:42:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:42:15: 5000000 INFO @ Sat, 24 Aug 2019 19:42:22: 2000000 INFO @ Sat, 24 Aug 2019 19:42:23: 6000000 INFO @ Sat, 24 Aug 2019 19:42:30: 3000000 INFO @ Sat, 24 Aug 2019 19:42:31: 7000000 INFO @ Sat, 24 Aug 2019 19:42:37: 4000000 INFO @ Sat, 24 Aug 2019 19:42:39: 8000000 INFO @ Sat, 24 Aug 2019 19:42:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:42:45: 5000000 INFO @ Sat, 24 Aug 2019 19:42:47: 9000000 INFO @ Sat, 24 Aug 2019 19:42:50: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:42:50: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:42:50: #1 total tags in treatment: 9261554 INFO @ Sat, 24 Aug 2019 19:42:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:42:50: #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 19:42:51: #1 tags after filtering in treatment: 9261407 INFO @ Sat, 24 Aug 2019 19:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:42:51: #1 finished! INFO @ Sat, 24 Aug 2019 19:42:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:42:54: #2 number of paired peaks: 12967 INFO @ Sat, 24 Aug 2019 19:42:54: start model_add_line... INFO @ Sat, 24 Aug 2019 19:42:54: start X-correlation... INFO @ Sat, 24 Aug 2019 19:42:54: end of X-cor INFO @ Sat, 24 Aug 2019 19:42:54: #2 finished! INFO @ Sat, 24 Aug 2019 19:42:54: #2 predicted fragment length is 46 bps INFO @ Sat, 24 Aug 2019 19:42:54: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 24 Aug 2019 19:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.10_model.r WARNING @ Sat, 24 Aug 2019 19:42:54: #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 19:42:54: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 24 Aug 2019 19:42:54: #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 19:42:54: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:42:55: 6000000 INFO @ Sat, 24 Aug 2019 19:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.05_summits.bed INFO @ Sat, 24 Aug 2019 19:43:00: Done! pass1 - making usageList (21 chroms): 2 millis pass2 - checking and writing primary data (214 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:43:01: 7000000 INFO @ Sat, 24 Aug 2019 19:43:08: 8000000 INFO @ Sat, 24 Aug 2019 19:43:15: 9000000 INFO @ Sat, 24 Aug 2019 19:43:16: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:43:16: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:43:16: #1 total tags in treatment: 9261554 INFO @ Sat, 24 Aug 2019 19:43:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:43:16: #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 19:43:17: #1 tags after filtering in treatment: 9261407 INFO @ Sat, 24 Aug 2019 19:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:43:17: #1 finished! INFO @ Sat, 24 Aug 2019 19:43:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:43:19: #2 number of paired peaks: 12967 INFO @ Sat, 24 Aug 2019 19:43:19: start model_add_line... INFO @ Sat, 24 Aug 2019 19:43:19: start X-correlation... INFO @ Sat, 24 Aug 2019 19:43:20: end of X-cor INFO @ Sat, 24 Aug 2019 19:43:20: #2 finished! INFO @ Sat, 24 Aug 2019 19:43:20: #2 predicted fragment length is 46 bps INFO @ Sat, 24 Aug 2019 19:43:20: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 24 Aug 2019 19:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.20_model.r WARNING @ Sat, 24 Aug 2019 19:43:20: #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 19:43:20: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 24 Aug 2019 19:43:20: #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 19:43:20: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:43:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:43:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:43:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:43:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:43:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.10_summits.bed INFO @ Sat, 24 Aug 2019 19:43:42: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:43:56: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094894/SRX5094894.20_summits.bed INFO @ Sat, 24 Aug 2019 19:44:13: 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。