Job ID = 2590348 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T11:53:32 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 ) 2019-08-12T11:53:32 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 ) spots read : 12,886,723 reads read : 25,773,446 reads written : 12,886,723 reads 0-length : 12,886,723 spots read : 12,700,490 reads read : 25,400,980 reads written : 12,700,490 reads 0-length : 12,700,490 spots read : 12,865,808 reads read : 25,731,616 reads written : 12,865,808 reads 0-length : 12,865,808 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: 00:10:29 38453021 reads; of these: 38453021 (100.00%) were unpaired; of these: 1456881 (3.79%) aligned 0 times 29779419 (77.44%) aligned exactly 1 time 7216721 (18.77%) aligned >1 times 96.21% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 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 16 files... [bam_rmdupse_core] 6035787 / 36996140 = 0.1631 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, 12 Aug 2019 21:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.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, 12 Aug 2019 21:26:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.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, 12 Aug 2019 21:26:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.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, 12 Aug 2019 21:26:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:27:00: 1000000 INFO @ Mon, 12 Aug 2019 21:27:01: 1000000 INFO @ Mon, 12 Aug 2019 21:27:02: 1000000 INFO @ Mon, 12 Aug 2019 21:27:09: 2000000 INFO @ Mon, 12 Aug 2019 21:27:09: 2000000 INFO @ Mon, 12 Aug 2019 21:27:09: 2000000 INFO @ Mon, 12 Aug 2019 21:27:16: 3000000 INFO @ Mon, 12 Aug 2019 21:27:17: 3000000 INFO @ Mon, 12 Aug 2019 21:27:17: 3000000 INFO @ Mon, 12 Aug 2019 21:27:23: 4000000 INFO @ Mon, 12 Aug 2019 21:27:24: 4000000 INFO @ Mon, 12 Aug 2019 21:27:26: 4000000 INFO @ Mon, 12 Aug 2019 21:27:31: 5000000 INFO @ Mon, 12 Aug 2019 21:27:32: 5000000 INFO @ Mon, 12 Aug 2019 21:27:35: 5000000 INFO @ Mon, 12 Aug 2019 21:27:38: 6000000 INFO @ Mon, 12 Aug 2019 21:27:39: 6000000 INFO @ Mon, 12 Aug 2019 21:27:43: 6000000 INFO @ Mon, 12 Aug 2019 21:27:46: 7000000 INFO @ Mon, 12 Aug 2019 21:27:47: 7000000 INFO @ Mon, 12 Aug 2019 21:27:52: 7000000 INFO @ Mon, 12 Aug 2019 21:27:54: 8000000 INFO @ Mon, 12 Aug 2019 21:27:55: 8000000 INFO @ Mon, 12 Aug 2019 21:28:02: 8000000 INFO @ Mon, 12 Aug 2019 21:28:03: 9000000 INFO @ Mon, 12 Aug 2019 21:28:03: 9000000 INFO @ Mon, 12 Aug 2019 21:28:11: 10000000 INFO @ Mon, 12 Aug 2019 21:28:11: 10000000 INFO @ Mon, 12 Aug 2019 21:28:13: 9000000 INFO @ Mon, 12 Aug 2019 21:28:19: 11000000 INFO @ Mon, 12 Aug 2019 21:28:19: 11000000 INFO @ Mon, 12 Aug 2019 21:28:24: 10000000 INFO @ Mon, 12 Aug 2019 21:28:26: 12000000 INFO @ Mon, 12 Aug 2019 21:28:27: 12000000 INFO @ Mon, 12 Aug 2019 21:28:34: 13000000 INFO @ Mon, 12 Aug 2019 21:28:34: 13000000 INFO @ Mon, 12 Aug 2019 21:28:35: 11000000 INFO @ Mon, 12 Aug 2019 21:28:42: 14000000 INFO @ Mon, 12 Aug 2019 21:28:42: 14000000 INFO @ Mon, 12 Aug 2019 21:28:45: 12000000 INFO @ Mon, 12 Aug 2019 21:28:50: 15000000 INFO @ Mon, 12 Aug 2019 21:28:50: 15000000 INFO @ Mon, 12 Aug 2019 21:28:56: 13000000 INFO @ Mon, 12 Aug 2019 21:28:58: 16000000 INFO @ Mon, 12 Aug 2019 21:28:58: 16000000 INFO @ Mon, 12 Aug 2019 21:29:05: 17000000 INFO @ Mon, 12 Aug 2019 21:29:05: 17000000 INFO @ Mon, 12 Aug 2019 21:29:06: 14000000 INFO @ Mon, 12 Aug 2019 21:29:13: 18000000 INFO @ Mon, 12 Aug 2019 21:29:13: 18000000 INFO @ Mon, 12 Aug 2019 21:29:17: 15000000 INFO @ Mon, 12 Aug 2019 21:29:21: 19000000 INFO @ Mon, 12 Aug 2019 21:29:21: 19000000 INFO @ Mon, 12 Aug 2019 21:29:27: 16000000 INFO @ Mon, 12 Aug 2019 21:29:28: 20000000 INFO @ Mon, 12 Aug 2019 21:29:28: 20000000 INFO @ Mon, 12 Aug 2019 21:29:36: 21000000 INFO @ Mon, 12 Aug 2019 21:29:36: 21000000 INFO @ Mon, 12 Aug 2019 21:29:37: 17000000 INFO @ Mon, 12 Aug 2019 21:29:44: 22000000 INFO @ Mon, 12 Aug 2019 21:29:44: 22000000 INFO @ Mon, 12 Aug 2019 21:29:48: 18000000 INFO @ Mon, 12 Aug 2019 21:29:51: 23000000 INFO @ Mon, 12 Aug 2019 21:29:51: 23000000 INFO @ Mon, 12 Aug 2019 21:29:58: 19000000 INFO @ Mon, 12 Aug 2019 21:29:59: 24000000 INFO @ Mon, 12 Aug 2019 21:29:59: 24000000 INFO @ Mon, 12 Aug 2019 21:30:07: 25000000 INFO @ Mon, 12 Aug 2019 21:30:07: 25000000 INFO @ Mon, 12 Aug 2019 21:30:08: 20000000 INFO @ Mon, 12 Aug 2019 21:30:15: 26000000 INFO @ Mon, 12 Aug 2019 21:30:15: 26000000 INFO @ Mon, 12 Aug 2019 21:30:18: 21000000 INFO @ Mon, 12 Aug 2019 21:30:22: 27000000 INFO @ Mon, 12 Aug 2019 21:30:22: 27000000 INFO @ Mon, 12 Aug 2019 21:30:28: 22000000 INFO @ Mon, 12 Aug 2019 21:30:30: 28000000 INFO @ Mon, 12 Aug 2019 21:30:30: 28000000 INFO @ Mon, 12 Aug 2019 21:30:37: 29000000 INFO @ Mon, 12 Aug 2019 21:30:37: 29000000 INFO @ Mon, 12 Aug 2019 21:30:38: 23000000 INFO @ Mon, 12 Aug 2019 21:30:45: 30000000 INFO @ Mon, 12 Aug 2019 21:30:45: 30000000 INFO @ Mon, 12 Aug 2019 21:30:48: 24000000 INFO @ Mon, 12 Aug 2019 21:30:52: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:30:52: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:30:52: #1 total tags in treatment: 30960353 INFO @ Mon, 12 Aug 2019 21:30:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:30:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:30:52: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:30:52: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:30:52: #1 total tags in treatment: 30960353 INFO @ Mon, 12 Aug 2019 21:30:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:30:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:30:53: #1 tags after filtering in treatment: 30960353 INFO @ Mon, 12 Aug 2019 21:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:30:53: #1 finished! INFO @ Mon, 12 Aug 2019 21:30:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:30:53: #1 tags after filtering in treatment: 30960353 INFO @ Mon, 12 Aug 2019 21:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:30:53: #1 finished! INFO @ Mon, 12 Aug 2019 21:30:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:30:55: #2 number of paired peaks: 398 WARNING @ Mon, 12 Aug 2019 21:30:55: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Mon, 12 Aug 2019 21:30:55: start model_add_line... INFO @ Mon, 12 Aug 2019 21:30:56: #2 number of paired peaks: 398 WARNING @ Mon, 12 Aug 2019 21:30:56: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Mon, 12 Aug 2019 21:30:56: start model_add_line... INFO @ Mon, 12 Aug 2019 21:30:56: start X-correlation... INFO @ Mon, 12 Aug 2019 21:30:56: end of X-cor INFO @ Mon, 12 Aug 2019 21:30:56: #2 finished! INFO @ Mon, 12 Aug 2019 21:30:56: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 21:30:56: #2 alternative fragment length(s) may be 4,134 bps INFO @ Mon, 12 Aug 2019 21:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.20_model.r INFO @ Mon, 12 Aug 2019 21:30:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:30:56: start X-correlation... INFO @ Mon, 12 Aug 2019 21:30:56: end of X-cor INFO @ Mon, 12 Aug 2019 21:30:56: #2 finished! INFO @ Mon, 12 Aug 2019 21:30:56: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 21:30:56: #2 alternative fragment length(s) may be 4,134 bps INFO @ Mon, 12 Aug 2019 21:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.10_model.r INFO @ Mon, 12 Aug 2019 21:30:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:30:58: 25000000 INFO @ Mon, 12 Aug 2019 21:31:08: 26000000 INFO @ Mon, 12 Aug 2019 21:31:18: 27000000 INFO @ Mon, 12 Aug 2019 21:31:28: 28000000 INFO @ Mon, 12 Aug 2019 21:31:38: 29000000 INFO @ Mon, 12 Aug 2019 21:31:47: 30000000 INFO @ Mon, 12 Aug 2019 21:31:57: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:31:57: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:31:57: #1 total tags in treatment: 30960353 INFO @ Mon, 12 Aug 2019 21:31:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:31:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:31:57: #1 tags after filtering in treatment: 30960353 INFO @ Mon, 12 Aug 2019 21:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:31:57: #1 finished! INFO @ Mon, 12 Aug 2019 21:31:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:32:00: #2 number of paired peaks: 398 WARNING @ Mon, 12 Aug 2019 21:32:00: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Mon, 12 Aug 2019 21:32:00: start model_add_line... INFO @ Mon, 12 Aug 2019 21:32:00: start X-correlation... INFO @ Mon, 12 Aug 2019 21:32:00: end of X-cor INFO @ Mon, 12 Aug 2019 21:32:00: #2 finished! INFO @ Mon, 12 Aug 2019 21:32:00: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 21:32:00: #2 alternative fragment length(s) may be 4,134 bps INFO @ Mon, 12 Aug 2019 21:32:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.05_model.r INFO @ Mon, 12 Aug 2019 21:32:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:32:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:32:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:32:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.20_summits.bed INFO @ Mon, 12 Aug 2019 21:32:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2559 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.10_summits.bed INFO @ Mon, 12 Aug 2019 21:32:47: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6604 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:33:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981622/SRX3981622.05_summits.bed INFO @ Mon, 12 Aug 2019 21:33:58: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (11042 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。