Job ID = 1307534 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:26:16 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 ) 2019-06-03T13:26:16 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 ) 2019-06-03T13:26:16 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 ) 2019-06-03T13:27:31 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 ) 2019-06-03T13:27:34 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 ) 2019-06-03T13:29:49 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 ) 2019-06-03T13:29:49 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 ) spots read : 23,028,434 reads read : 46,056,868 reads written : 23,028,434 reads 0-length : 23,028,434 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:18 23028434 reads; of these: 23028434 (100.00%) were unpaired; of these: 996222 (4.33%) aligned 0 times 14923998 (64.81%) aligned exactly 1 time 7108214 (30.87%) aligned >1 times 95.67% overall alignment rate Time searching: 00:15:18 Overall time: 00:15:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2687713 / 22032212 = 0.1220 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 22:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:55:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:55:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:55:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:55:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:55:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:55:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:55:43: 1000000 INFO @ Mon, 03 Jun 2019 22:55:44: 1000000 INFO @ Mon, 03 Jun 2019 22:55:45: 1000000 INFO @ Mon, 03 Jun 2019 22:55:52: 2000000 INFO @ Mon, 03 Jun 2019 22:55:54: 2000000 INFO @ Mon, 03 Jun 2019 22:55:55: 2000000 INFO @ Mon, 03 Jun 2019 22:56:01: 3000000 INFO @ Mon, 03 Jun 2019 22:56:04: 3000000 INFO @ Mon, 03 Jun 2019 22:56:06: 3000000 INFO @ Mon, 03 Jun 2019 22:56:09: 4000000 INFO @ Mon, 03 Jun 2019 22:56:13: 4000000 INFO @ Mon, 03 Jun 2019 22:56:17: 4000000 INFO @ Mon, 03 Jun 2019 22:56:17: 5000000 INFO @ Mon, 03 Jun 2019 22:56:23: 5000000 INFO @ Mon, 03 Jun 2019 22:56:25: 6000000 INFO @ Mon, 03 Jun 2019 22:56:27: 5000000 INFO @ Mon, 03 Jun 2019 22:56:32: 6000000 INFO @ Mon, 03 Jun 2019 22:56:34: 7000000 INFO @ Mon, 03 Jun 2019 22:56:38: 6000000 INFO @ Mon, 03 Jun 2019 22:56:41: 7000000 INFO @ Mon, 03 Jun 2019 22:56:42: 8000000 INFO @ Mon, 03 Jun 2019 22:56:48: 7000000 INFO @ Mon, 03 Jun 2019 22:56:50: 9000000 INFO @ Mon, 03 Jun 2019 22:56:50: 8000000 INFO @ Mon, 03 Jun 2019 22:56:59: 8000000 INFO @ Mon, 03 Jun 2019 22:56:59: 10000000 INFO @ Mon, 03 Jun 2019 22:57:00: 9000000 INFO @ Mon, 03 Jun 2019 22:57:07: 11000000 INFO @ Mon, 03 Jun 2019 22:57:09: 9000000 INFO @ Mon, 03 Jun 2019 22:57:09: 10000000 INFO @ Mon, 03 Jun 2019 22:57:15: 12000000 INFO @ Mon, 03 Jun 2019 22:57:19: 11000000 INFO @ Mon, 03 Jun 2019 22:57:20: 10000000 INFO @ Mon, 03 Jun 2019 22:57:23: 13000000 INFO @ Mon, 03 Jun 2019 22:57:28: 12000000 INFO @ Mon, 03 Jun 2019 22:57:29: 11000000 INFO @ Mon, 03 Jun 2019 22:57:31: 14000000 INFO @ Mon, 03 Jun 2019 22:57:37: 13000000 INFO @ Mon, 03 Jun 2019 22:57:39: 12000000 INFO @ Mon, 03 Jun 2019 22:57:40: 15000000 INFO @ Mon, 03 Jun 2019 22:57:46: 14000000 INFO @ Mon, 03 Jun 2019 22:57:48: 13000000 INFO @ Mon, 03 Jun 2019 22:57:48: 16000000 INFO @ Mon, 03 Jun 2019 22:57:55: 15000000 INFO @ Mon, 03 Jun 2019 22:57:56: 17000000 INFO @ Mon, 03 Jun 2019 22:57:57: 14000000 INFO @ Mon, 03 Jun 2019 22:58:04: 18000000 INFO @ Mon, 03 Jun 2019 22:58:04: 16000000 INFO @ Mon, 03 Jun 2019 22:58:07: 15000000 INFO @ Mon, 03 Jun 2019 22:58:12: 19000000 INFO @ Mon, 03 Jun 2019 22:58:13: 17000000 INFO @ Mon, 03 Jun 2019 22:58:15: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:58:15: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:58:15: #1 total tags in treatment: 19344499 INFO @ Mon, 03 Jun 2019 22:58:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:58:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:58:15: #1 tags after filtering in treatment: 19344499 INFO @ Mon, 03 Jun 2019 22:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:58:15: #1 finished! INFO @ Mon, 03 Jun 2019 22:58:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:58:16: 16000000 INFO @ Mon, 03 Jun 2019 22:58:17: #2 number of paired peaks: 184 WARNING @ Mon, 03 Jun 2019 22:58:17: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 03 Jun 2019 22:58:17: start model_add_line... INFO @ Mon, 03 Jun 2019 22:58:17: start X-correlation... INFO @ Mon, 03 Jun 2019 22:58:17: end of X-cor INFO @ Mon, 03 Jun 2019 22:58:17: #2 finished! INFO @ Mon, 03 Jun 2019 22:58:17: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 22:58:17: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 22:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.05_model.r WARNING @ Mon, 03 Jun 2019 22:58:17: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:58:17: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 22:58:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:58:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:58:22: 18000000 INFO @ Mon, 03 Jun 2019 22:58:25: 17000000 INFO @ Mon, 03 Jun 2019 22:58:31: 19000000 INFO @ Mon, 03 Jun 2019 22:58:34: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:58:34: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:58:34: #1 total tags in treatment: 19344499 INFO @ Mon, 03 Jun 2019 22:58:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:58:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:58:34: 18000000 INFO @ Mon, 03 Jun 2019 22:58:34: #1 tags after filtering in treatment: 19344499 INFO @ Mon, 03 Jun 2019 22:58:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:58:34: #1 finished! INFO @ Mon, 03 Jun 2019 22:58:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:58:36: #2 number of paired peaks: 184 WARNING @ Mon, 03 Jun 2019 22:58:36: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 03 Jun 2019 22:58:36: start model_add_line... INFO @ Mon, 03 Jun 2019 22:58:36: start X-correlation... INFO @ Mon, 03 Jun 2019 22:58:36: end of X-cor INFO @ Mon, 03 Jun 2019 22:58:36: #2 finished! INFO @ Mon, 03 Jun 2019 22:58:36: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 22:58:36: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 22:58:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.20_model.r WARNING @ Mon, 03 Jun 2019 22:58:36: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:58:36: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 22:58:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:58:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:58:45: 19000000 INFO @ Mon, 03 Jun 2019 22:58:48: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:58:48: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:58:48: #1 total tags in treatment: 19344499 INFO @ Mon, 03 Jun 2019 22:58:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:58:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:58:49: #1 tags after filtering in treatment: 19344499 INFO @ Mon, 03 Jun 2019 22:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:58:49: #1 finished! INFO @ Mon, 03 Jun 2019 22:58:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:58:50: #2 number of paired peaks: 184 WARNING @ Mon, 03 Jun 2019 22:58:50: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 03 Jun 2019 22:58:50: start model_add_line... INFO @ Mon, 03 Jun 2019 22:58:50: start X-correlation... INFO @ Mon, 03 Jun 2019 22:58:50: end of X-cor INFO @ Mon, 03 Jun 2019 22:58:50: #2 finished! INFO @ Mon, 03 Jun 2019 22:58:50: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 22:58:50: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 22:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.10_model.r WARNING @ Mon, 03 Jun 2019 22:58:50: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:58:50: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 22:58:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:58:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:59:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:59:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.05_summits.bed INFO @ Mon, 03 Jun 2019 22:59:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1853 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:59:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:59:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:59:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:59:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.20_summits.bed INFO @ Mon, 03 Jun 2019 22:59:54: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1060 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343092/SRX5343092.10_summits.bed INFO @ Mon, 03 Jun 2019 23:00:08: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1457 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。