Job ID = 2640426 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:34:08 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 ) 2019-08-24T07:34:49 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 ) 2019-08-24T07:34:49 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 ) 2019-08-24T07:40:36 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 ) 2019-08-24T07:34:49 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 ) 2019-08-24T07:43:31 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 ) 2019-08-24T07:44:14 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 ) 2019-08-24T07:45:12 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 : 175,918,353 reads read : 175,918,353 reads written : 175,918,353 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR980342.sra.cache’: 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: 04:22:48 175918353 reads; of these: 175918353 (100.00%) were unpaired; of these: 45934259 (26.11%) aligned 0 times 106264880 (60.41%) aligned exactly 1 time 23719214 (13.48%) aligned >1 times 73.89% overall alignment rate Time searching: 04:22:51 Overall time: 04:22:51 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 56 files... [bam_rmdupse_core] 103858852 / 129984094 = 0.7990 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.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 21:48:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:48:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:48:26: 1000000 INFO @ Sat, 24 Aug 2019 21:48:33: 2000000 INFO @ Sat, 24 Aug 2019 21:48:40: 3000000 INFO @ Sat, 24 Aug 2019 21:48:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.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 21:48:47: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:48:47: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:48:48: 4000000 INFO @ Sat, 24 Aug 2019 21:48:55: 5000000 INFO @ Sat, 24 Aug 2019 21:48:55: 1000000 INFO @ Sat, 24 Aug 2019 21:49:02: 6000000 INFO @ Sat, 24 Aug 2019 21:49:03: 2000000 INFO @ Sat, 24 Aug 2019 21:49:09: 7000000 INFO @ Sat, 24 Aug 2019 21:49:12: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:49:16: 8000000 INFO @ Sat, 24 Aug 2019 21:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.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 21:49:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:49:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:49:20: 4000000 INFO @ Sat, 24 Aug 2019 21:49:23: 9000000 INFO @ Sat, 24 Aug 2019 21:49:26: 1000000 INFO @ Sat, 24 Aug 2019 21:49:28: 5000000 INFO @ Sat, 24 Aug 2019 21:49:31: 10000000 INFO @ Sat, 24 Aug 2019 21:49:35: 2000000 INFO @ Sat, 24 Aug 2019 21:49:36: 6000000 INFO @ Sat, 24 Aug 2019 21:49:38: 11000000 INFO @ Sat, 24 Aug 2019 21:49:43: 3000000 INFO @ Sat, 24 Aug 2019 21:49:44: 7000000 INFO @ Sat, 24 Aug 2019 21:49:45: 12000000 INFO @ Sat, 24 Aug 2019 21:49:52: 4000000 INFO @ Sat, 24 Aug 2019 21:49:53: 8000000 INFO @ Sat, 24 Aug 2019 21:49:53: 13000000 INFO @ Sat, 24 Aug 2019 21:50:00: 5000000 INFO @ Sat, 24 Aug 2019 21:50:01: 14000000 INFO @ Sat, 24 Aug 2019 21:50:01: 9000000 INFO @ Sat, 24 Aug 2019 21:50:08: 15000000 INFO @ Sat, 24 Aug 2019 21:50:09: 6000000 INFO @ Sat, 24 Aug 2019 21:50:09: 10000000 INFO @ Sat, 24 Aug 2019 21:50:16: 16000000 INFO @ Sat, 24 Aug 2019 21:50:17: 7000000 INFO @ Sat, 24 Aug 2019 21:50:17: 11000000 INFO @ Sat, 24 Aug 2019 21:50:24: 17000000 INFO @ Sat, 24 Aug 2019 21:50:25: 8000000 INFO @ Sat, 24 Aug 2019 21:50:26: 12000000 INFO @ Sat, 24 Aug 2019 21:50:32: 18000000 INFO @ Sat, 24 Aug 2019 21:50:34: 9000000 INFO @ Sat, 24 Aug 2019 21:50:34: 13000000 INFO @ Sat, 24 Aug 2019 21:50:39: 19000000 INFO @ Sat, 24 Aug 2019 21:50:42: 10000000 INFO @ Sat, 24 Aug 2019 21:50:43: 14000000 INFO @ Sat, 24 Aug 2019 21:50:47: 20000000 INFO @ Sat, 24 Aug 2019 21:50:50: 11000000 INFO @ Sat, 24 Aug 2019 21:50:52: 15000000 INFO @ Sat, 24 Aug 2019 21:50:54: 21000000 INFO @ Sat, 24 Aug 2019 21:50:58: 12000000 INFO @ Sat, 24 Aug 2019 21:51:01: 16000000 INFO @ Sat, 24 Aug 2019 21:51:02: 22000000 INFO @ Sat, 24 Aug 2019 21:51:07: 13000000 INFO @ Sat, 24 Aug 2019 21:51:09: 23000000 INFO @ Sat, 24 Aug 2019 21:51:09: 17000000 INFO @ Sat, 24 Aug 2019 21:51:16: 14000000 INFO @ Sat, 24 Aug 2019 21:51:17: 24000000 INFO @ Sat, 24 Aug 2019 21:51:18: 18000000 INFO @ Sat, 24 Aug 2019 21:51:24: 25000000 INFO @ Sat, 24 Aug 2019 21:51:25: 15000000 INFO @ Sat, 24 Aug 2019 21:51:27: 19000000 INFO @ Sat, 24 Aug 2019 21:51:31: 26000000 INFO @ Sat, 24 Aug 2019 21:51:33: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:51:33: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:51:33: #1 total tags in treatment: 26125242 INFO @ Sat, 24 Aug 2019 21:51:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:51:33: #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 21:51:33: #1 tags after filtering in treatment: 26125121 INFO @ Sat, 24 Aug 2019 21:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:51:33: #1 finished! INFO @ Sat, 24 Aug 2019 21:51:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:51:34: 16000000 INFO @ Sat, 24 Aug 2019 21:51:36: 20000000 INFO @ Sat, 24 Aug 2019 21:51:39: #2 number of paired peaks: 61109 INFO @ Sat, 24 Aug 2019 21:51:39: start model_add_line... INFO @ Sat, 24 Aug 2019 21:51:39: start X-correlation... INFO @ Sat, 24 Aug 2019 21:51:39: end of X-cor INFO @ Sat, 24 Aug 2019 21:51:39: #2 finished! INFO @ Sat, 24 Aug 2019 21:51:39: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 21:51:39: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 21:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.05_model.r WARNING @ Sat, 24 Aug 2019 21:51:39: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:51:39: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 24 Aug 2019 21:51:39: #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 21:51:39: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:51:42: 17000000 INFO @ Sat, 24 Aug 2019 21:51:44: 21000000 INFO @ Sat, 24 Aug 2019 21:51:51: 18000000 INFO @ Sat, 24 Aug 2019 21:51:52: 22000000 INFO @ Sat, 24 Aug 2019 21:52:00: 19000000 INFO @ Sat, 24 Aug 2019 21:52:01: 23000000 INFO @ Sat, 24 Aug 2019 21:52:09: 20000000 INFO @ Sat, 24 Aug 2019 21:52:09: 24000000 INFO @ Sat, 24 Aug 2019 21:52:17: 21000000 INFO @ Sat, 24 Aug 2019 21:52:17: 25000000 INFO @ Sat, 24 Aug 2019 21:52:25: 22000000 INFO @ Sat, 24 Aug 2019 21:52:26: 26000000 INFO @ Sat, 24 Aug 2019 21:52:27: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:52:27: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:52:27: #1 total tags in treatment: 26125242 INFO @ Sat, 24 Aug 2019 21:52:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:52:27: #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 21:52:28: #1 tags after filtering in treatment: 26125121 INFO @ Sat, 24 Aug 2019 21:52:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:52:28: #1 finished! INFO @ Sat, 24 Aug 2019 21:52:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:52:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:52:33: 23000000 INFO @ Sat, 24 Aug 2019 21:52:34: #2 number of paired peaks: 61109 INFO @ Sat, 24 Aug 2019 21:52:34: start model_add_line... INFO @ Sat, 24 Aug 2019 21:52:34: start X-correlation... INFO @ Sat, 24 Aug 2019 21:52:34: end of X-cor INFO @ Sat, 24 Aug 2019 21:52:34: #2 finished! INFO @ Sat, 24 Aug 2019 21:52:34: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 21:52:34: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 21:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.10_model.r WARNING @ Sat, 24 Aug 2019 21:52:34: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:52:34: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 24 Aug 2019 21:52:34: #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 21:52:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:52:42: 24000000 INFO @ Sat, 24 Aug 2019 21:52:49: 25000000 INFO @ Sat, 24 Aug 2019 21:52:57: 26000000 INFO @ Sat, 24 Aug 2019 21:52:59: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:52:59: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:52:59: #1 total tags in treatment: 26125242 INFO @ Sat, 24 Aug 2019 21:52:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:52:59: #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 21:52:59: #1 tags after filtering in treatment: 26125121 INFO @ Sat, 24 Aug 2019 21:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:52:59: #1 finished! INFO @ Sat, 24 Aug 2019 21:52:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:53:01: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:53:05: #2 number of paired peaks: 61109 INFO @ Sat, 24 Aug 2019 21:53:05: start model_add_line... INFO @ Sat, 24 Aug 2019 21:53:05: start X-correlation... INFO @ Sat, 24 Aug 2019 21:53:05: end of X-cor INFO @ Sat, 24 Aug 2019 21:53:05: #2 finished! INFO @ Sat, 24 Aug 2019 21:53:05: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 21:53:05: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 21:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.20_model.r WARNING @ Sat, 24 Aug 2019 21:53:05: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:53:05: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 24 Aug 2019 21:53:05: #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 21:53:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.05_peaks.xls INFO @ Sat, 24 Aug 2019 21:53:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.05_summits.bed INFO @ Sat, 24 Aug 2019 21:53:47: Done! pass1 - making usageList (232 chroms): 19 millis pass2 - checking and writing primary data (75487 records, 4 fields): 101 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:53:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:55:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:56:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.10_peaks.xls INFO @ Sat, 24 Aug 2019 21:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.10_summits.bed INFO @ Sat, 24 Aug 2019 21:56:09: Done! pass1 - making usageList (168 chroms): 16 millis pass2 - checking and writing primary data (45299 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.20_peaks.xls INFO @ Sat, 24 Aug 2019 21:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349431/SRX349431.20_summits.bed INFO @ Sat, 24 Aug 2019 21:56:37: Done! pass1 - making usageList (115 chroms): 8 millis pass2 - checking and writing primary data (25718 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。