Job ID = 1295112 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:02:52 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 ) 2019-06-03T03:10:49 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 ) 2019-06-03T03:10:49 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 ) 2019-06-03T03:10:49 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 : 40,444,037 reads read : 40,444,037 reads written : 40,444,037 2019-06-03T03:30:41 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 ) 2019-06-03T03:30:41 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 ) 2019-06-03T03:30:41 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 ) 2019-06-03T03:30:41 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 ) 2019-06-03T03:30:41 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 ) 2019-06-03T03:30:41 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 : 44,380,544 reads read : 44,380,544 reads written : 44,380,544 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:04 84824581 reads; of these: 84824581 (100.00%) were unpaired; of these: 4756613 (5.61%) aligned 0 times 61295945 (72.26%) aligned exactly 1 time 18772023 (22.13%) aligned >1 times 94.39% overall alignment rate Time searching: 00:26:05 Overall time: 00:26:05 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 36 files... [bam_rmdupse_core] 42641747 / 80067968 = 0.5326 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 13:26:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.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 13:26:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:26:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:26:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.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 13:26:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.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 13:26:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:26:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:26:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:26:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:26:31: 1000000 INFO @ Mon, 03 Jun 2019 13:26:32: 1000000 INFO @ Mon, 03 Jun 2019 13:26:32: 1000000 INFO @ Mon, 03 Jun 2019 13:26:40: 2000000 INFO @ Mon, 03 Jun 2019 13:26:40: 2000000 INFO @ Mon, 03 Jun 2019 13:26:40: 2000000 INFO @ Mon, 03 Jun 2019 13:26:48: 3000000 INFO @ Mon, 03 Jun 2019 13:26:48: 3000000 INFO @ Mon, 03 Jun 2019 13:26:49: 3000000 INFO @ Mon, 03 Jun 2019 13:26:55: 4000000 INFO @ Mon, 03 Jun 2019 13:26:55: 4000000 INFO @ Mon, 03 Jun 2019 13:26:58: 4000000 INFO @ Mon, 03 Jun 2019 13:27:03: 5000000 INFO @ Mon, 03 Jun 2019 13:27:03: 5000000 INFO @ Mon, 03 Jun 2019 13:27:06: 5000000 INFO @ Mon, 03 Jun 2019 13:27:12: 6000000 INFO @ Mon, 03 Jun 2019 13:27:12: 6000000 INFO @ Mon, 03 Jun 2019 13:27:13: 6000000 INFO @ Mon, 03 Jun 2019 13:27:21: 7000000 INFO @ Mon, 03 Jun 2019 13:27:21: 7000000 INFO @ Mon, 03 Jun 2019 13:27:21: 7000000 INFO @ Mon, 03 Jun 2019 13:27:28: 8000000 INFO @ Mon, 03 Jun 2019 13:27:28: 8000000 INFO @ Mon, 03 Jun 2019 13:27:29: 8000000 INFO @ Mon, 03 Jun 2019 13:27:36: 9000000 INFO @ Mon, 03 Jun 2019 13:27:36: 9000000 INFO @ Mon, 03 Jun 2019 13:27:38: 9000000 INFO @ Mon, 03 Jun 2019 13:27:44: 10000000 INFO @ Mon, 03 Jun 2019 13:27:44: 10000000 INFO @ Mon, 03 Jun 2019 13:27:46: 10000000 INFO @ Mon, 03 Jun 2019 13:27:52: 11000000 INFO @ Mon, 03 Jun 2019 13:27:52: 11000000 INFO @ Mon, 03 Jun 2019 13:27:55: 11000000 INFO @ Mon, 03 Jun 2019 13:28:02: 12000000 INFO @ Mon, 03 Jun 2019 13:28:02: 12000000 INFO @ Mon, 03 Jun 2019 13:28:06: 12000000 INFO @ Mon, 03 Jun 2019 13:28:09: 13000000 INFO @ Mon, 03 Jun 2019 13:28:09: 13000000 INFO @ Mon, 03 Jun 2019 13:28:15: 13000000 INFO @ Mon, 03 Jun 2019 13:28:16: 14000000 INFO @ Mon, 03 Jun 2019 13:28:17: 14000000 INFO @ Mon, 03 Jun 2019 13:28:23: 15000000 INFO @ Mon, 03 Jun 2019 13:28:24: 15000000 INFO @ Mon, 03 Jun 2019 13:28:24: 14000000 INFO @ Mon, 03 Jun 2019 13:28:31: 16000000 INFO @ Mon, 03 Jun 2019 13:28:31: 16000000 INFO @ Mon, 03 Jun 2019 13:28:33: 15000000 INFO @ Mon, 03 Jun 2019 13:28:38: 17000000 INFO @ Mon, 03 Jun 2019 13:28:38: 17000000 INFO @ Mon, 03 Jun 2019 13:28:41: 16000000 INFO @ Mon, 03 Jun 2019 13:28:45: 18000000 INFO @ Mon, 03 Jun 2019 13:28:45: 18000000 INFO @ Mon, 03 Jun 2019 13:28:50: 17000000 INFO @ Mon, 03 Jun 2019 13:28:52: 19000000 INFO @ Mon, 03 Jun 2019 13:28:52: 19000000 INFO @ Mon, 03 Jun 2019 13:28:58: 18000000 INFO @ Mon, 03 Jun 2019 13:28:59: 20000000 INFO @ Mon, 03 Jun 2019 13:28:59: 20000000 INFO @ Mon, 03 Jun 2019 13:29:06: 21000000 INFO @ Mon, 03 Jun 2019 13:29:06: 19000000 INFO @ Mon, 03 Jun 2019 13:29:07: 21000000 INFO @ Mon, 03 Jun 2019 13:29:13: 22000000 INFO @ Mon, 03 Jun 2019 13:29:14: 22000000 INFO @ Mon, 03 Jun 2019 13:29:15: 20000000 INFO @ Mon, 03 Jun 2019 13:29:21: 23000000 INFO @ Mon, 03 Jun 2019 13:29:21: 23000000 INFO @ Mon, 03 Jun 2019 13:29:23: 21000000 INFO @ Mon, 03 Jun 2019 13:29:28: 24000000 INFO @ Mon, 03 Jun 2019 13:29:29: 24000000 INFO @ Mon, 03 Jun 2019 13:29:32: 22000000 INFO @ Mon, 03 Jun 2019 13:29:36: 25000000 INFO @ Mon, 03 Jun 2019 13:29:36: 25000000 INFO @ Mon, 03 Jun 2019 13:29:42: 23000000 INFO @ Mon, 03 Jun 2019 13:29:43: 26000000 INFO @ Mon, 03 Jun 2019 13:29:43: 26000000 INFO @ Mon, 03 Jun 2019 13:29:50: 24000000 INFO @ Mon, 03 Jun 2019 13:29:51: 27000000 INFO @ Mon, 03 Jun 2019 13:29:51: 27000000 INFO @ Mon, 03 Jun 2019 13:29:58: 28000000 INFO @ Mon, 03 Jun 2019 13:29:58: 28000000 INFO @ Mon, 03 Jun 2019 13:29:59: 25000000 INFO @ Mon, 03 Jun 2019 13:30:05: 29000000 INFO @ Mon, 03 Jun 2019 13:30:05: 29000000 INFO @ Mon, 03 Jun 2019 13:30:08: 26000000 INFO @ Mon, 03 Jun 2019 13:30:12: 30000000 INFO @ Mon, 03 Jun 2019 13:30:13: 30000000 INFO @ Mon, 03 Jun 2019 13:30:16: 27000000 INFO @ Mon, 03 Jun 2019 13:30:20: 31000000 INFO @ Mon, 03 Jun 2019 13:30:20: 31000000 INFO @ Mon, 03 Jun 2019 13:30:25: 28000000 INFO @ Mon, 03 Jun 2019 13:30:27: 32000000 INFO @ Mon, 03 Jun 2019 13:30:27: 32000000 INFO @ Mon, 03 Jun 2019 13:30:34: 29000000 INFO @ Mon, 03 Jun 2019 13:30:34: 33000000 INFO @ Mon, 03 Jun 2019 13:30:35: 33000000 INFO @ Mon, 03 Jun 2019 13:30:41: 34000000 INFO @ Mon, 03 Jun 2019 13:30:42: 34000000 INFO @ Mon, 03 Jun 2019 13:30:42: 30000000 INFO @ Mon, 03 Jun 2019 13:30:48: 35000000 INFO @ Mon, 03 Jun 2019 13:30:49: 35000000 INFO @ Mon, 03 Jun 2019 13:30:51: 31000000 INFO @ Mon, 03 Jun 2019 13:30:55: 36000000 INFO @ Mon, 03 Jun 2019 13:30:56: 36000000 INFO @ Mon, 03 Jun 2019 13:31:00: 32000000 INFO @ Mon, 03 Jun 2019 13:31:03: 37000000 INFO @ Mon, 03 Jun 2019 13:31:04: 37000000 INFO @ Mon, 03 Jun 2019 13:31:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:31:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:31:06: #1 total tags in treatment: 37426221 INFO @ Mon, 03 Jun 2019 13:31:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:31:06: #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 13:31:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:31:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:31:07: #1 total tags in treatment: 37426221 INFO @ Mon, 03 Jun 2019 13:31:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:31:07: #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 13:31:07: #1 tags after filtering in treatment: 37426221 INFO @ Mon, 03 Jun 2019 13:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:31:07: #1 finished! INFO @ Mon, 03 Jun 2019 13:31:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:31:08: #1 tags after filtering in treatment: 37426221 INFO @ Mon, 03 Jun 2019 13:31:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:31:08: #1 finished! INFO @ Mon, 03 Jun 2019 13:31:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:31:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:31:09: 33000000 INFO @ Mon, 03 Jun 2019 13:31:10: #2 number of paired peaks: 729 WARNING @ Mon, 03 Jun 2019 13:31:10: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 03 Jun 2019 13:31:10: start model_add_line... INFO @ Mon, 03 Jun 2019 13:31:11: start X-correlation... INFO @ Mon, 03 Jun 2019 13:31:11: end of X-cor INFO @ Mon, 03 Jun 2019 13:31:11: #2 finished! INFO @ Mon, 03 Jun 2019 13:31:11: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 13:31:11: #2 alternative fragment length(s) may be 4,136 bps INFO @ Mon, 03 Jun 2019 13:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.20_model.r INFO @ Mon, 03 Jun 2019 13:31:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:31:11: #2 number of paired peaks: 729 WARNING @ Mon, 03 Jun 2019 13:31:11: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 03 Jun 2019 13:31:11: start model_add_line... INFO @ Mon, 03 Jun 2019 13:31:11: start X-correlation... INFO @ Mon, 03 Jun 2019 13:31:11: end of X-cor INFO @ Mon, 03 Jun 2019 13:31:11: #2 finished! INFO @ Mon, 03 Jun 2019 13:31:11: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 13:31:11: #2 alternative fragment length(s) may be 4,136 bps INFO @ Mon, 03 Jun 2019 13:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.05_model.r INFO @ Mon, 03 Jun 2019 13:31:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:31:17: 34000000 INFO @ Mon, 03 Jun 2019 13:31:26: 35000000 INFO @ Mon, 03 Jun 2019 13:31:35: 36000000 INFO @ Mon, 03 Jun 2019 13:31:43: 37000000 INFO @ Mon, 03 Jun 2019 13:31:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:31:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:31:47: #1 total tags in treatment: 37426221 INFO @ Mon, 03 Jun 2019 13:31:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:31:47: #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 13:31:48: #1 tags after filtering in treatment: 37426221 INFO @ Mon, 03 Jun 2019 13:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:31:48: #1 finished! INFO @ Mon, 03 Jun 2019 13:31:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:31:51: #2 number of paired peaks: 729 WARNING @ Mon, 03 Jun 2019 13:31:51: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 03 Jun 2019 13:31:51: start model_add_line... INFO @ Mon, 03 Jun 2019 13:31:52: start X-correlation... INFO @ Mon, 03 Jun 2019 13:31:52: end of X-cor INFO @ Mon, 03 Jun 2019 13:31:52: #2 finished! INFO @ Mon, 03 Jun 2019 13:31:52: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 13:31:52: #2 alternative fragment length(s) may be 4,136 bps INFO @ Mon, 03 Jun 2019 13:31:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.10_model.r INFO @ Mon, 03 Jun 2019 13:31:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:31:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:32:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:32:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:33:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.20_summits.bed INFO @ Mon, 03 Jun 2019 13:33:34: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8331 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:33:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:33:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:33:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.05_summits.bed INFO @ Mon, 03 Jun 2019 13:33:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12760 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318811/SRX318811.10_summits.bed INFO @ Mon, 03 Jun 2019 13:34:12: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10627 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。