Job ID = 1307443 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:24:14 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 ) 2019-06-03T13:24:14 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 ) 2019-06-03T13:24:14 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 ) 2019-06-03T13:26:16 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 ) spots read : 23,028,437 reads read : 46,056,874 reads written : 23,028,437 reads 0-length : 23,028,437 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: 00:13:42 23028437 reads; of these: 23028437 (100.00%) were unpaired; of these: 996235 (4.33%) aligned 0 times 14923978 (64.81%) aligned exactly 1 time 7108224 (30.87%) aligned >1 times 95.67% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 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] 2687013 / 22032202 = 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 22:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.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 22:50:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:50:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.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 22:50:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:50:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.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 22:50:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:50:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:50:54: 1000000 INFO @ Mon, 03 Jun 2019 22:50:56: 1000000 INFO @ Mon, 03 Jun 2019 22:50:58: 1000000 INFO @ Mon, 03 Jun 2019 22:51:02: 2000000 INFO @ Mon, 03 Jun 2019 22:51:06: 2000000 INFO @ Mon, 03 Jun 2019 22:51:09: 3000000 INFO @ Mon, 03 Jun 2019 22:51:09: 2000000 INFO @ Mon, 03 Jun 2019 22:51:15: 3000000 INFO @ Mon, 03 Jun 2019 22:51:15: 4000000 INFO @ Mon, 03 Jun 2019 22:51:19: 3000000 INFO @ Mon, 03 Jun 2019 22:51:22: 5000000 INFO @ Mon, 03 Jun 2019 22:51:23: 4000000 INFO @ Mon, 03 Jun 2019 22:51:29: 4000000 INFO @ Mon, 03 Jun 2019 22:51:29: 6000000 INFO @ Mon, 03 Jun 2019 22:51:32: 5000000 INFO @ Mon, 03 Jun 2019 22:51:36: 7000000 INFO @ Mon, 03 Jun 2019 22:51:39: 5000000 INFO @ Mon, 03 Jun 2019 22:51:40: 6000000 INFO @ Mon, 03 Jun 2019 22:51:43: 8000000 INFO @ Mon, 03 Jun 2019 22:51:49: 7000000 INFO @ Mon, 03 Jun 2019 22:51:49: 6000000 INFO @ Mon, 03 Jun 2019 22:51:50: 9000000 INFO @ Mon, 03 Jun 2019 22:51:57: 10000000 INFO @ Mon, 03 Jun 2019 22:51:58: 8000000 INFO @ Mon, 03 Jun 2019 22:51:59: 7000000 INFO @ Mon, 03 Jun 2019 22:52:04: 11000000 INFO @ Mon, 03 Jun 2019 22:52:07: 9000000 INFO @ Mon, 03 Jun 2019 22:52:09: 8000000 INFO @ Mon, 03 Jun 2019 22:52:11: 12000000 INFO @ Mon, 03 Jun 2019 22:52:16: 10000000 INFO @ Mon, 03 Jun 2019 22:52:17: 13000000 INFO @ Mon, 03 Jun 2019 22:52:19: 9000000 INFO @ Mon, 03 Jun 2019 22:52:24: 11000000 INFO @ Mon, 03 Jun 2019 22:52:24: 14000000 INFO @ Mon, 03 Jun 2019 22:52:29: 10000000 INFO @ Mon, 03 Jun 2019 22:52:31: 15000000 INFO @ Mon, 03 Jun 2019 22:52:33: 12000000 INFO @ Mon, 03 Jun 2019 22:52:38: 16000000 INFO @ Mon, 03 Jun 2019 22:52:38: 11000000 INFO @ Mon, 03 Jun 2019 22:52:42: 13000000 INFO @ Mon, 03 Jun 2019 22:52:45: 17000000 INFO @ Mon, 03 Jun 2019 22:52:48: 12000000 INFO @ Mon, 03 Jun 2019 22:52:50: 14000000 INFO @ Mon, 03 Jun 2019 22:52:53: 18000000 INFO @ Mon, 03 Jun 2019 22:52:58: 13000000 INFO @ Mon, 03 Jun 2019 22:52:59: 15000000 INFO @ Mon, 03 Jun 2019 22:53:00: 19000000 INFO @ Mon, 03 Jun 2019 22:53:02: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:02: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:02: #1 total tags in treatment: 19345189 INFO @ Mon, 03 Jun 2019 22:53:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:02: #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 22:53:03: #1 tags after filtering in treatment: 19345189 INFO @ Mon, 03 Jun 2019 22:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:03: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:04: #2 number of paired peaks: 164 WARNING @ Mon, 03 Jun 2019 22:53:04: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 03 Jun 2019 22:53:04: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:04: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:04: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:04: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:04: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 22:53:04: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 22:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.10_model.r WARNING @ Mon, 03 Jun 2019 22:53:04: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:53:04: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 22:53:04: #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 22:53:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:53:08: 14000000 INFO @ Mon, 03 Jun 2019 22:53:08: 16000000 INFO @ Mon, 03 Jun 2019 22:53:17: 15000000 INFO @ Mon, 03 Jun 2019 22:53:18: 17000000 INFO @ Mon, 03 Jun 2019 22:53:27: 18000000 INFO @ Mon, 03 Jun 2019 22:53:28: 16000000 INFO @ Mon, 03 Jun 2019 22:53:36: 19000000 INFO @ Mon, 03 Jun 2019 22:53:38: 17000000 INFO @ Mon, 03 Jun 2019 22:53:39: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:39: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:39: #1 total tags in treatment: 19345189 INFO @ Mon, 03 Jun 2019 22:53:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:39: #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 22:53:39: #1 tags after filtering in treatment: 19345189 INFO @ Mon, 03 Jun 2019 22:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:39: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:41: #2 number of paired peaks: 164 WARNING @ Mon, 03 Jun 2019 22:53:41: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 03 Jun 2019 22:53:41: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:41: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:41: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:41: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:41: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 22:53:41: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 22:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.05_model.r WARNING @ Mon, 03 Jun 2019 22:53:41: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:53:41: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 22:53:41: #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 22:53:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:53:49: 18000000 INFO @ Mon, 03 Jun 2019 22:53:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:53:58: 19000000 INFO @ Mon, 03 Jun 2019 22:54:01: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:54:01: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:54:01: #1 total tags in treatment: 19345189 INFO @ Mon, 03 Jun 2019 22:54:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:54:01: #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 22:54:01: #1 tags after filtering in treatment: 19345189 INFO @ Mon, 03 Jun 2019 22:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:54:01: #1 finished! INFO @ Mon, 03 Jun 2019 22:54:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:54:03: #2 number of paired peaks: 164 WARNING @ Mon, 03 Jun 2019 22:54:03: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 03 Jun 2019 22:54:03: start model_add_line... INFO @ Mon, 03 Jun 2019 22:54:03: start X-correlation... INFO @ Mon, 03 Jun 2019 22:54:03: end of X-cor INFO @ Mon, 03 Jun 2019 22:54:03: #2 finished! INFO @ Mon, 03 Jun 2019 22:54:03: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 22:54:03: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 22:54:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.20_model.r WARNING @ Mon, 03 Jun 2019 22:54:03: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:54:03: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 22:54:03: #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 22:54:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:54:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:54:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.10_summits.bed INFO @ Mon, 03 Jun 2019 22:54:17: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1430 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:54:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:54:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:54:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.05_summits.bed INFO @ Mon, 03 Jun 2019 22:54:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1866 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343084/SRX5343084.20_summits.bed INFO @ Mon, 03 Jun 2019 22:55:16: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1071 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。