Job ID = 1294431 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:42:40 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 ) 2019-06-02T22:42:40 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 ) 2019-06-02T22:42:40 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 ) 2019-06-02T22:42:40 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 ) 2019-06-02T22:42:40 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 ) 2019-06-02T22:44:33 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 ) 2019-06-02T22:44:33 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 ) 2019-06-02T22:44:33 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 ) 2019-06-02T22:44:33 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 ) 2019-06-02T22:44:33 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 ) 2019-06-02T22:48:28 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 ) 2019-06-02T22:52:11 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 ) 2019-06-02T22:52:11 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 ) spots read : 21,552,956 reads read : 21,552,956 reads written : 21,552,956 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: 00:06:55 21552956 reads; of these: 21552956 (100.00%) were unpaired; of these: 1153436 (5.35%) aligned 0 times 17077559 (79.24%) aligned exactly 1 time 3321961 (15.41%) aligned >1 times 94.65% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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] 3661673 / 20399520 = 0.1795 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 08:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.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 08:07:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:07:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.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 08:07:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:07:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.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 08:07:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:07:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:07:48: 1000000 INFO @ Mon, 03 Jun 2019 08:07:50: 1000000 INFO @ Mon, 03 Jun 2019 08:07:50: 1000000 INFO @ Mon, 03 Jun 2019 08:07:55: 2000000 INFO @ Mon, 03 Jun 2019 08:07:59: 2000000 INFO @ Mon, 03 Jun 2019 08:08:00: 2000000 INFO @ Mon, 03 Jun 2019 08:08:03: 3000000 INFO @ Mon, 03 Jun 2019 08:08:09: 3000000 INFO @ Mon, 03 Jun 2019 08:08:10: 3000000 INFO @ Mon, 03 Jun 2019 08:08:11: 4000000 INFO @ Mon, 03 Jun 2019 08:08:19: 5000000 INFO @ Mon, 03 Jun 2019 08:08:19: 4000000 INFO @ Mon, 03 Jun 2019 08:08:20: 4000000 INFO @ Mon, 03 Jun 2019 08:08:26: 6000000 INFO @ Mon, 03 Jun 2019 08:08:28: 5000000 INFO @ Mon, 03 Jun 2019 08:08:29: 5000000 INFO @ Mon, 03 Jun 2019 08:08:33: 7000000 INFO @ Mon, 03 Jun 2019 08:08:37: 6000000 INFO @ Mon, 03 Jun 2019 08:08:38: 6000000 INFO @ Mon, 03 Jun 2019 08:08:41: 8000000 INFO @ Mon, 03 Jun 2019 08:08:46: 7000000 INFO @ Mon, 03 Jun 2019 08:08:48: 7000000 INFO @ Mon, 03 Jun 2019 08:08:48: 9000000 INFO @ Mon, 03 Jun 2019 08:08:55: 10000000 INFO @ Mon, 03 Jun 2019 08:08:56: 8000000 INFO @ Mon, 03 Jun 2019 08:08:56: 8000000 INFO @ Mon, 03 Jun 2019 08:09:03: 11000000 INFO @ Mon, 03 Jun 2019 08:09:05: 9000000 INFO @ Mon, 03 Jun 2019 08:09:05: 9000000 INFO @ Mon, 03 Jun 2019 08:09:10: 12000000 INFO @ Mon, 03 Jun 2019 08:09:14: 10000000 INFO @ Mon, 03 Jun 2019 08:09:15: 10000000 INFO @ Mon, 03 Jun 2019 08:09:17: 13000000 INFO @ Mon, 03 Jun 2019 08:09:23: 11000000 INFO @ Mon, 03 Jun 2019 08:09:24: 11000000 INFO @ Mon, 03 Jun 2019 08:09:25: 14000000 INFO @ Mon, 03 Jun 2019 08:09:31: 12000000 INFO @ Mon, 03 Jun 2019 08:09:32: 15000000 INFO @ Mon, 03 Jun 2019 08:09:33: 12000000 INFO @ Mon, 03 Jun 2019 08:09:39: 16000000 INFO @ Mon, 03 Jun 2019 08:09:40: 13000000 INFO @ Mon, 03 Jun 2019 08:09:42: 13000000 INFO @ Mon, 03 Jun 2019 08:09:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:09:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:09:45: #1 total tags in treatment: 16737847 INFO @ Mon, 03 Jun 2019 08:09:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:09:45: #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 08:09:45: #1 tags after filtering in treatment: 16737847 INFO @ Mon, 03 Jun 2019 08:09:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:09:45: #1 finished! INFO @ Mon, 03 Jun 2019 08:09:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:09:47: #2 number of paired peaks: 469 WARNING @ Mon, 03 Jun 2019 08:09:47: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 03 Jun 2019 08:09:47: start model_add_line... INFO @ Mon, 03 Jun 2019 08:09:47: start X-correlation... INFO @ Mon, 03 Jun 2019 08:09:47: end of X-cor INFO @ Mon, 03 Jun 2019 08:09:47: #2 finished! INFO @ Mon, 03 Jun 2019 08:09:47: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 08:09:47: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 08:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.05_model.r INFO @ Mon, 03 Jun 2019 08:09:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:09:50: 14000000 INFO @ Mon, 03 Jun 2019 08:09:51: 14000000 INFO @ Mon, 03 Jun 2019 08:09:58: 15000000 INFO @ Mon, 03 Jun 2019 08:10:00: 15000000 INFO @ Mon, 03 Jun 2019 08:10:07: 16000000 INFO @ Mon, 03 Jun 2019 08:10:09: 16000000 INFO @ Mon, 03 Jun 2019 08:10:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:10:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:10:14: #1 total tags in treatment: 16737847 INFO @ Mon, 03 Jun 2019 08:10:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:10:14: #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 08:10:14: #1 tags after filtering in treatment: 16737847 INFO @ Mon, 03 Jun 2019 08:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:10:14: #1 finished! INFO @ Mon, 03 Jun 2019 08:10:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:10:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:10:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:10:15: #1 total tags in treatment: 16737847 INFO @ Mon, 03 Jun 2019 08:10:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:10:15: #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 08:10:16: #1 tags after filtering in treatment: 16737847 INFO @ Mon, 03 Jun 2019 08:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:10:16: #1 finished! INFO @ Mon, 03 Jun 2019 08:10:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:10:16: #2 number of paired peaks: 469 WARNING @ Mon, 03 Jun 2019 08:10:16: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 03 Jun 2019 08:10:16: start model_add_line... INFO @ Mon, 03 Jun 2019 08:10:16: start X-correlation... INFO @ Mon, 03 Jun 2019 08:10:16: end of X-cor INFO @ Mon, 03 Jun 2019 08:10:16: #2 finished! INFO @ Mon, 03 Jun 2019 08:10:16: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 08:10:16: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 08:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.20_model.r INFO @ Mon, 03 Jun 2019 08:10:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:10:17: #2 number of paired peaks: 469 WARNING @ Mon, 03 Jun 2019 08:10:17: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 03 Jun 2019 08:10:17: start model_add_line... INFO @ Mon, 03 Jun 2019 08:10:17: start X-correlation... INFO @ Mon, 03 Jun 2019 08:10:17: end of X-cor INFO @ Mon, 03 Jun 2019 08:10:17: #2 finished! INFO @ Mon, 03 Jun 2019 08:10:17: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 08:10:17: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 08:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.10_model.r INFO @ Mon, 03 Jun 2019 08:10:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:10:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:10:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:10:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:10:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.05_summits.bed INFO @ Mon, 03 Jun 2019 08:10:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5304 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:11:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:11:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.20_summits.bed INFO @ Mon, 03 Jun 2019 08:11:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (927 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287600/SRX287600.10_summits.bed INFO @ Mon, 03 Jun 2019 08:11:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2440 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。