Job ID = 2640405 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:18:06 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 ) 2019-08-24T07:18:06 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 ) 2019-08-24T07:40:31 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 ) 2019-08-24T07:40:31 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 ) 2019-08-24T07:44:07 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 ) 2019-08-24T07:44:11 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 ) 2019-08-24T07:45:24 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 ) 2019-08-24T07:46:30 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 ) 2019-08-24T07:49:05 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 : 72,300,118 reads read : 72,300,118 reads written : 72,300,118 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: 00:49:42 72300118 reads; of these: 72300118 (100.00%) were unpaired; of these: 20682375 (28.61%) aligned 0 times 35726774 (49.41%) aligned exactly 1 time 15890969 (21.98%) aligned >1 times 71.39% overall alignment rate Time searching: 00:49:45 Overall time: 00:49:45 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 24 files... [bam_rmdupse_core] 17182727 / 51617743 = 0.3329 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.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 17:57:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:57:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:57:39: 1000000 INFO @ Sat, 24 Aug 2019 17:57:47: 2000000 INFO @ Sat, 24 Aug 2019 17:57:54: 3000000 INFO @ Sat, 24 Aug 2019 17:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.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 17:58:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:58:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:58:01: 4000000 INFO @ Sat, 24 Aug 2019 17:58:09: 5000000 INFO @ Sat, 24 Aug 2019 17:58:10: 1000000 INFO @ Sat, 24 Aug 2019 17:58:16: 6000000 INFO @ Sat, 24 Aug 2019 17:58:18: 2000000 INFO @ Sat, 24 Aug 2019 17:58:24: 7000000 INFO @ Sat, 24 Aug 2019 17:58:27: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:58:31: 8000000 INFO @ Sat, 24 Aug 2019 17:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.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 17:58:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:58:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:58:35: 4000000 INFO @ Sat, 24 Aug 2019 17:58:39: 9000000 INFO @ Sat, 24 Aug 2019 17:58:40: 1000000 INFO @ Sat, 24 Aug 2019 17:58:44: 5000000 INFO @ Sat, 24 Aug 2019 17:58:46: 10000000 INFO @ Sat, 24 Aug 2019 17:58:48: 2000000 INFO @ Sat, 24 Aug 2019 17:58:53: 6000000 INFO @ Sat, 24 Aug 2019 17:58:54: 11000000 INFO @ Sat, 24 Aug 2019 17:58:57: 3000000 INFO @ Sat, 24 Aug 2019 17:59:01: 12000000 INFO @ Sat, 24 Aug 2019 17:59:01: 7000000 INFO @ Sat, 24 Aug 2019 17:59:05: 4000000 INFO @ Sat, 24 Aug 2019 17:59:09: 13000000 INFO @ Sat, 24 Aug 2019 17:59:10: 8000000 INFO @ Sat, 24 Aug 2019 17:59:14: 5000000 INFO @ Sat, 24 Aug 2019 17:59:16: 14000000 INFO @ Sat, 24 Aug 2019 17:59:19: 9000000 INFO @ Sat, 24 Aug 2019 17:59:22: 6000000 INFO @ Sat, 24 Aug 2019 17:59:23: 15000000 INFO @ Sat, 24 Aug 2019 17:59:27: 10000000 INFO @ Sat, 24 Aug 2019 17:59:30: 7000000 INFO @ Sat, 24 Aug 2019 17:59:31: 16000000 INFO @ Sat, 24 Aug 2019 17:59:36: 11000000 INFO @ Sat, 24 Aug 2019 17:59:38: 17000000 INFO @ Sat, 24 Aug 2019 17:59:39: 8000000 INFO @ Sat, 24 Aug 2019 17:59:44: 12000000 INFO @ Sat, 24 Aug 2019 17:59:46: 18000000 INFO @ Sat, 24 Aug 2019 17:59:47: 9000000 INFO @ Sat, 24 Aug 2019 17:59:53: 13000000 INFO @ Sat, 24 Aug 2019 17:59:53: 19000000 INFO @ Sat, 24 Aug 2019 17:59:55: 10000000 INFO @ Sat, 24 Aug 2019 18:00:01: 20000000 INFO @ Sat, 24 Aug 2019 18:00:01: 14000000 INFO @ Sat, 24 Aug 2019 18:00:04: 11000000 INFO @ Sat, 24 Aug 2019 18:00:08: 21000000 INFO @ Sat, 24 Aug 2019 18:00:10: 15000000 INFO @ Sat, 24 Aug 2019 18:00:12: 12000000 INFO @ Sat, 24 Aug 2019 18:00:16: 22000000 INFO @ Sat, 24 Aug 2019 18:00:18: 16000000 INFO @ Sat, 24 Aug 2019 18:00:20: 13000000 INFO @ Sat, 24 Aug 2019 18:00:23: 23000000 INFO @ Sat, 24 Aug 2019 18:00:27: 17000000 INFO @ Sat, 24 Aug 2019 18:00:29: 14000000 INFO @ Sat, 24 Aug 2019 18:00:31: 24000000 INFO @ Sat, 24 Aug 2019 18:00:35: 18000000 INFO @ Sat, 24 Aug 2019 18:00:37: 15000000 INFO @ Sat, 24 Aug 2019 18:00:38: 25000000 INFO @ Sat, 24 Aug 2019 18:00:43: 19000000 INFO @ Sat, 24 Aug 2019 18:00:46: 26000000 INFO @ Sat, 24 Aug 2019 18:00:46: 16000000 INFO @ Sat, 24 Aug 2019 18:00:52: 20000000 INFO @ Sat, 24 Aug 2019 18:00:53: 27000000 INFO @ Sat, 24 Aug 2019 18:00:54: 17000000 INFO @ Sat, 24 Aug 2019 18:01:02: 21000000 INFO @ Sat, 24 Aug 2019 18:01:03: 28000000 INFO @ Sat, 24 Aug 2019 18:01:05: 18000000 INFO @ Sat, 24 Aug 2019 18:01:10: 29000000 INFO @ Sat, 24 Aug 2019 18:01:10: 22000000 INFO @ Sat, 24 Aug 2019 18:01:13: 19000000 INFO @ Sat, 24 Aug 2019 18:01:18: 30000000 INFO @ Sat, 24 Aug 2019 18:01:19: 23000000 INFO @ Sat, 24 Aug 2019 18:01:22: 20000000 INFO @ Sat, 24 Aug 2019 18:01:25: 31000000 INFO @ Sat, 24 Aug 2019 18:01:27: 24000000 INFO @ Sat, 24 Aug 2019 18:01:30: 21000000 INFO @ Sat, 24 Aug 2019 18:01:33: 32000000 INFO @ Sat, 24 Aug 2019 18:01:36: 25000000 INFO @ Sat, 24 Aug 2019 18:01:38: 22000000 INFO @ Sat, 24 Aug 2019 18:01:41: 33000000 INFO @ Sat, 24 Aug 2019 18:01:44: 26000000 INFO @ Sat, 24 Aug 2019 18:01:47: 23000000 INFO @ Sat, 24 Aug 2019 18:01:49: 34000000 INFO @ Sat, 24 Aug 2019 18:01:52: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 18:01:52: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 18:01:52: #1 total tags in treatment: 34435016 INFO @ Sat, 24 Aug 2019 18:01:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:01:52: #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 18:01:53: #1 tags after filtering in treatment: 34434949 INFO @ Sat, 24 Aug 2019 18:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:01:53: #1 finished! INFO @ Sat, 24 Aug 2019 18:01:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:01:53: 27000000 INFO @ Sat, 24 Aug 2019 18:01:56: 24000000 INFO @ Sat, 24 Aug 2019 18:01:57: #2 number of paired peaks: 6654 INFO @ Sat, 24 Aug 2019 18:01:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:01:57: start X-correlation... INFO @ Sat, 24 Aug 2019 18:01:57: end of X-cor INFO @ Sat, 24 Aug 2019 18:01:57: #2 finished! INFO @ Sat, 24 Aug 2019 18:01:57: #2 predicted fragment length is 49 bps INFO @ Sat, 24 Aug 2019 18:01:57: #2 alternative fragment length(s) may be 49,218,411,523 bps INFO @ Sat, 24 Aug 2019 18:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.05_model.r WARNING @ Sat, 24 Aug 2019 18:01:57: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:01:57: #2 You may need to consider one of the other alternative d(s): 49,218,411,523 WARNING @ Sat, 24 Aug 2019 18:01:57: #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 18:01:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:01:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:02:02: 28000000 INFO @ Sat, 24 Aug 2019 18:02:05: 25000000 INFO @ Sat, 24 Aug 2019 18:02:11: 29000000 INFO @ Sat, 24 Aug 2019 18:02:14: 26000000 INFO @ Sat, 24 Aug 2019 18:02:19: 30000000 INFO @ Sat, 24 Aug 2019 18:02:22: 27000000 INFO @ Sat, 24 Aug 2019 18:02:28: 31000000 INFO @ Sat, 24 Aug 2019 18:02:31: 28000000 INFO @ Sat, 24 Aug 2019 18:02:37: 32000000 INFO @ Sat, 24 Aug 2019 18:02:40: 29000000 INFO @ Sat, 24 Aug 2019 18:02:46: 33000000 INFO @ Sat, 24 Aug 2019 18:02:49: 30000000 INFO @ Sat, 24 Aug 2019 18:02:55: 34000000 INFO @ Sat, 24 Aug 2019 18:02:57: 31000000 INFO @ Sat, 24 Aug 2019 18:02:59: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 18:02:59: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 18:02:59: #1 total tags in treatment: 34435016 INFO @ Sat, 24 Aug 2019 18:02:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:02:59: #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 18:03:00: #1 tags after filtering in treatment: 34434949 INFO @ Sat, 24 Aug 2019 18:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:03:00: #1 finished! INFO @ Sat, 24 Aug 2019 18:03:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:03:04: #2 number of paired peaks: 6654 INFO @ Sat, 24 Aug 2019 18:03:04: start model_add_line... INFO @ Sat, 24 Aug 2019 18:03:04: start X-correlation... INFO @ Sat, 24 Aug 2019 18:03:04: end of X-cor INFO @ Sat, 24 Aug 2019 18:03:04: #2 finished! INFO @ Sat, 24 Aug 2019 18:03:04: #2 predicted fragment length is 49 bps INFO @ Sat, 24 Aug 2019 18:03:04: #2 alternative fragment length(s) may be 49,218,411,523 bps INFO @ Sat, 24 Aug 2019 18:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.10_model.r WARNING @ Sat, 24 Aug 2019 18:03:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:03:04: #2 You may need to consider one of the other alternative d(s): 49,218,411,523 WARNING @ Sat, 24 Aug 2019 18:03:04: #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 18:03:04: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:03:05: 32000000 INFO @ Sat, 24 Aug 2019 18:03:13: 33000000 INFO @ Sat, 24 Aug 2019 18:03:21: 34000000 INFO @ Sat, 24 Aug 2019 18:03:25: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 18:03:25: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 18:03:25: #1 total tags in treatment: 34435016 INFO @ Sat, 24 Aug 2019 18:03:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:03:25: #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 18:03:26: #1 tags after filtering in treatment: 34434949 INFO @ Sat, 24 Aug 2019 18:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:03:26: #1 finished! INFO @ Sat, 24 Aug 2019 18:03:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:03:30: #2 number of paired peaks: 6654 INFO @ Sat, 24 Aug 2019 18:03:30: start model_add_line... INFO @ Sat, 24 Aug 2019 18:03:30: start X-correlation... INFO @ Sat, 24 Aug 2019 18:03:30: end of X-cor INFO @ Sat, 24 Aug 2019 18:03:30: #2 finished! INFO @ Sat, 24 Aug 2019 18:03:30: #2 predicted fragment length is 49 bps INFO @ Sat, 24 Aug 2019 18:03:30: #2 alternative fragment length(s) may be 49,218,411,523 bps INFO @ Sat, 24 Aug 2019 18:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.20_model.r WARNING @ Sat, 24 Aug 2019 18:03:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:03:30: #2 You may need to consider one of the other alternative d(s): 49,218,411,523 WARNING @ Sat, 24 Aug 2019 18:03:30: #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 18:03:30: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:03:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.05_summits.bed INFO @ Sat, 24 Aug 2019 18:04:38: Done! pass1 - making usageList (78 chroms): 3 millis pass2 - checking and writing primary data (7062 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:04:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:05:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:05:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:05:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:05:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.10_summits.bed INFO @ Sat, 24 Aug 2019 18:05:43: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (3569 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:06:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337080/ERX337080.20_summits.bed INFO @ Sat, 24 Aug 2019 18:06:10: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1313 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。