Job ID = 1303739 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:30:51 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 ) 2019-06-03T11:31:14 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 ) 2019-06-03T11:31:29 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 ) 2019-06-03T11:31:29 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 ) 2019-06-03T11:32:20 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 ) 2019-06-03T11:34:00 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 ) 2019-06-03T11:35:32 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 ) 2019-06-03T11:35:32 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 ) 2019-06-03T11:36:20 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 ) 2019-06-03T11:38:35 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 ) 2019-06-03T11:39:33 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 ) spots read : 20,294,177 reads read : 40,588,354 reads written : 20,294,177 reads 0-length : 20,294,177 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: 00:14:52 20294177 reads; of these: 20294177 (100.00%) were unpaired; of these: 8514993 (41.96%) aligned 0 times 4212022 (20.75%) aligned exactly 1 time 7567162 (37.29%) aligned >1 times 58.04% overall alignment rate Time searching: 00:14:52 Overall time: 00:14:52 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 8 files... [bam_rmdupse_core] 7086672 / 11779184 = 0.6016 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 20:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.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 20:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.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 20:58:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:58:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:58:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:58:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.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 20:58:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:58:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:59:06: 1000000 INFO @ Mon, 03 Jun 2019 20:59:06: 1000000 INFO @ Mon, 03 Jun 2019 20:59:08: 1000000 INFO @ Mon, 03 Jun 2019 20:59:16: 2000000 INFO @ Mon, 03 Jun 2019 20:59:16: 2000000 INFO @ Mon, 03 Jun 2019 20:59:19: 2000000 INFO @ Mon, 03 Jun 2019 20:59:25: 3000000 INFO @ Mon, 03 Jun 2019 20:59:25: 3000000 INFO @ Mon, 03 Jun 2019 20:59:30: 3000000 INFO @ Mon, 03 Jun 2019 20:59:34: 4000000 INFO @ Mon, 03 Jun 2019 20:59:35: 4000000 INFO @ Mon, 03 Jun 2019 20:59:40: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 20:59:40: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 20:59:40: #1 total tags in treatment: 4692512 INFO @ Mon, 03 Jun 2019 20:59:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:59:40: #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 20:59:40: #1 tags after filtering in treatment: 4692512 INFO @ Mon, 03 Jun 2019 20:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:59:40: #1 finished! INFO @ Mon, 03 Jun 2019 20:59:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:59:40: #2 number of paired peaks: 2055 INFO @ Mon, 03 Jun 2019 20:59:40: start model_add_line... INFO @ Mon, 03 Jun 2019 20:59:40: start X-correlation... INFO @ Mon, 03 Jun 2019 20:59:41: end of X-cor INFO @ Mon, 03 Jun 2019 20:59:41: #2 finished! INFO @ Mon, 03 Jun 2019 20:59:41: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 20:59:41: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 20:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.05_model.r WARNING @ Mon, 03 Jun 2019 20:59:41: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:59:41: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 20:59:41: #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 20:59:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:59:41: 4000000 INFO @ Mon, 03 Jun 2019 20:59:41: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 20:59:41: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 20:59:41: #1 total tags in treatment: 4692512 INFO @ Mon, 03 Jun 2019 20:59:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:59:41: #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 20:59:41: #1 tags after filtering in treatment: 4692512 INFO @ Mon, 03 Jun 2019 20:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:59:41: #1 finished! INFO @ Mon, 03 Jun 2019 20:59:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:59:42: #2 number of paired peaks: 2055 INFO @ Mon, 03 Jun 2019 20:59:42: start model_add_line... INFO @ Mon, 03 Jun 2019 20:59:42: start X-correlation... INFO @ Mon, 03 Jun 2019 20:59:42: end of X-cor INFO @ Mon, 03 Jun 2019 20:59:42: #2 finished! INFO @ Mon, 03 Jun 2019 20:59:42: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 20:59:42: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 20:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.10_model.r WARNING @ Mon, 03 Jun 2019 20:59:42: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:59:42: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 20:59:42: #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 20:59:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:59:48: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 20:59:48: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 20:59:48: #1 total tags in treatment: 4692512 INFO @ Mon, 03 Jun 2019 20:59:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:59:48: #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 20:59:48: #1 tags after filtering in treatment: 4692512 INFO @ Mon, 03 Jun 2019 20:59:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:59:48: #1 finished! INFO @ Mon, 03 Jun 2019 20:59:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:59:49: #2 number of paired peaks: 2055 INFO @ Mon, 03 Jun 2019 20:59:49: start model_add_line... INFO @ Mon, 03 Jun 2019 20:59:49: start X-correlation... INFO @ Mon, 03 Jun 2019 20:59:49: end of X-cor INFO @ Mon, 03 Jun 2019 20:59:49: #2 finished! INFO @ Mon, 03 Jun 2019 20:59:49: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 20:59:49: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 20:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.20_model.r WARNING @ Mon, 03 Jun 2019 20:59:49: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:59:49: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 03 Jun 2019 20:59:49: #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 20:59:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:59:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:59:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.05_summits.bed INFO @ Mon, 03 Jun 2019 21:00:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2819 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:00:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.10_summits.bed INFO @ Mon, 03 Jun 2019 21:00:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1834 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941151/SRX4941151.20_summits.bed INFO @ Mon, 03 Jun 2019 21:00:10: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (867 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。