Job ID = 1292365 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T09:19:42 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 ) 2019-06-02T09:19:42 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 ) 2019-06-02T09:20:37 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 : 35,816,431 reads read : 71,632,862 reads written : 71,632,862 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: 00:47:18 35816431 reads; of these: 35816431 (100.00%) were paired; of these: 3327124 (9.29%) aligned concordantly 0 times 30425162 (84.95%) aligned concordantly exactly 1 time 2064145 (5.76%) aligned concordantly >1 times ---- 3327124 pairs aligned concordantly 0 times; of these: 1422809 (42.76%) aligned discordantly 1 time ---- 1904315 pairs aligned 0 times concordantly or discordantly; of these: 3808630 mates make up the pairs; of these: 2737528 (71.88%) aligned 0 times 761612 (20.00%) aligned exactly 1 time 309490 (8.13%) aligned >1 times 96.18% overall alignment rate Time searching: 00:47:18 Overall time: 00:47:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 32 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 13701889 / 33768702 = 0.4058 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 @ Sun, 02 Jun 2019 19:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:50:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:50:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:50:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:50:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:50:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:50:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:50:34: 1000000 INFO @ Sun, 02 Jun 2019 19:50:34: 1000000 INFO @ Sun, 02 Jun 2019 19:50:36: 1000000 INFO @ Sun, 02 Jun 2019 19:50:43: 2000000 INFO @ Sun, 02 Jun 2019 19:50:45: 2000000 INFO @ Sun, 02 Jun 2019 19:50:47: 2000000 INFO @ Sun, 02 Jun 2019 19:50:53: 3000000 INFO @ Sun, 02 Jun 2019 19:50:55: 3000000 INFO @ Sun, 02 Jun 2019 19:50:59: 3000000 INFO @ Sun, 02 Jun 2019 19:51:03: 4000000 INFO @ Sun, 02 Jun 2019 19:51:05: 4000000 INFO @ Sun, 02 Jun 2019 19:51:10: 4000000 INFO @ Sun, 02 Jun 2019 19:51:13: 5000000 INFO @ Sun, 02 Jun 2019 19:51:16: 5000000 INFO @ Sun, 02 Jun 2019 19:51:21: 5000000 INFO @ Sun, 02 Jun 2019 19:51:23: 6000000 INFO @ Sun, 02 Jun 2019 19:51:26: 6000000 INFO @ Sun, 02 Jun 2019 19:51:32: 7000000 INFO @ Sun, 02 Jun 2019 19:51:32: 6000000 INFO @ Sun, 02 Jun 2019 19:51:36: 7000000 INFO @ Sun, 02 Jun 2019 19:51:42: 8000000 INFO @ Sun, 02 Jun 2019 19:51:44: 7000000 INFO @ Sun, 02 Jun 2019 19:51:45: 8000000 INFO @ Sun, 02 Jun 2019 19:51:51: 9000000 INFO @ Sun, 02 Jun 2019 19:51:54: 8000000 INFO @ Sun, 02 Jun 2019 19:51:55: 9000000 INFO @ Sun, 02 Jun 2019 19:51:59: 10000000 INFO @ Sun, 02 Jun 2019 19:52:04: 10000000 INFO @ Sun, 02 Jun 2019 19:52:04: 9000000 INFO @ Sun, 02 Jun 2019 19:52:08: 11000000 INFO @ Sun, 02 Jun 2019 19:52:13: 11000000 INFO @ Sun, 02 Jun 2019 19:52:15: 10000000 INFO @ Sun, 02 Jun 2019 19:52:17: 12000000 INFO @ Sun, 02 Jun 2019 19:52:22: 12000000 INFO @ Sun, 02 Jun 2019 19:52:25: 11000000 INFO @ Sun, 02 Jun 2019 19:52:26: 13000000 INFO @ Sun, 02 Jun 2019 19:52:31: 13000000 INFO @ Sun, 02 Jun 2019 19:52:35: 14000000 INFO @ Sun, 02 Jun 2019 19:52:35: 12000000 INFO @ Sun, 02 Jun 2019 19:52:40: 14000000 INFO @ Sun, 02 Jun 2019 19:52:44: 15000000 INFO @ Sun, 02 Jun 2019 19:52:45: 13000000 INFO @ Sun, 02 Jun 2019 19:52:49: 15000000 INFO @ Sun, 02 Jun 2019 19:52:53: 16000000 INFO @ Sun, 02 Jun 2019 19:52:55: 14000000 INFO @ Sun, 02 Jun 2019 19:52:57: 16000000 INFO @ Sun, 02 Jun 2019 19:53:02: 17000000 INFO @ Sun, 02 Jun 2019 19:53:06: 15000000 INFO @ Sun, 02 Jun 2019 19:53:06: 17000000 INFO @ Sun, 02 Jun 2019 19:53:12: 18000000 INFO @ Sun, 02 Jun 2019 19:53:15: 18000000 INFO @ Sun, 02 Jun 2019 19:53:16: 16000000 INFO @ Sun, 02 Jun 2019 19:53:22: 19000000 INFO @ Sun, 02 Jun 2019 19:53:24: 19000000 INFO @ Sun, 02 Jun 2019 19:53:25: 17000000 INFO @ Sun, 02 Jun 2019 19:53:31: 20000000 INFO @ Sun, 02 Jun 2019 19:53:32: 20000000 INFO @ Sun, 02 Jun 2019 19:53:36: 18000000 INFO @ Sun, 02 Jun 2019 19:53:41: 21000000 INFO @ Sun, 02 Jun 2019 19:53:42: 21000000 INFO @ Sun, 02 Jun 2019 19:53:47: 19000000 INFO @ Sun, 02 Jun 2019 19:53:53: 22000000 INFO @ Sun, 02 Jun 2019 19:53:54: 22000000 INFO @ Sun, 02 Jun 2019 19:53:57: 20000000 INFO @ Sun, 02 Jun 2019 19:54:03: 23000000 INFO @ Sun, 02 Jun 2019 19:54:04: 23000000 INFO @ Sun, 02 Jun 2019 19:54:08: 21000000 INFO @ Sun, 02 Jun 2019 19:54:12: 24000000 INFO @ Sun, 02 Jun 2019 19:54:14: 24000000 INFO @ Sun, 02 Jun 2019 19:54:18: 22000000 INFO @ Sun, 02 Jun 2019 19:54:21: 25000000 INFO @ Sun, 02 Jun 2019 19:54:23: 25000000 INFO @ Sun, 02 Jun 2019 19:54:28: 23000000 INFO @ Sun, 02 Jun 2019 19:54:29: 26000000 INFO @ Sun, 02 Jun 2019 19:54:32: 26000000 INFO @ Sun, 02 Jun 2019 19:54:38: 27000000 INFO @ Sun, 02 Jun 2019 19:54:39: 24000000 INFO @ Sun, 02 Jun 2019 19:54:41: 27000000 INFO @ Sun, 02 Jun 2019 19:54:47: 28000000 INFO @ Sun, 02 Jun 2019 19:54:49: 25000000 INFO @ Sun, 02 Jun 2019 19:54:51: 28000000 INFO @ Sun, 02 Jun 2019 19:54:56: 29000000 INFO @ Sun, 02 Jun 2019 19:54:59: 26000000 INFO @ Sun, 02 Jun 2019 19:55:00: 29000000 INFO @ Sun, 02 Jun 2019 19:55:04: 30000000 INFO @ Sun, 02 Jun 2019 19:55:08: 27000000 INFO @ Sun, 02 Jun 2019 19:55:09: 30000000 INFO @ Sun, 02 Jun 2019 19:55:13: 31000000 INFO @ Sun, 02 Jun 2019 19:55:18: 28000000 INFO @ Sun, 02 Jun 2019 19:55:18: 31000000 INFO @ Sun, 02 Jun 2019 19:55:21: 32000000 INFO @ Sun, 02 Jun 2019 19:55:27: 32000000 INFO @ Sun, 02 Jun 2019 19:55:28: 29000000 INFO @ Sun, 02 Jun 2019 19:55:30: 33000000 INFO @ Sun, 02 Jun 2019 19:55:36: 33000000 INFO @ Sun, 02 Jun 2019 19:55:37: 30000000 INFO @ Sun, 02 Jun 2019 19:55:39: 34000000 INFO @ Sun, 02 Jun 2019 19:55:45: 34000000 INFO @ Sun, 02 Jun 2019 19:55:47: 31000000 INFO @ Sun, 02 Jun 2019 19:55:47: 35000000 INFO @ Sun, 02 Jun 2019 19:55:54: 35000000 INFO @ Sun, 02 Jun 2019 19:55:56: 36000000 INFO @ Sun, 02 Jun 2019 19:55:57: 32000000 INFO @ Sun, 02 Jun 2019 19:56:03: 36000000 INFO @ Sun, 02 Jun 2019 19:56:04: 37000000 INFO @ Sun, 02 Jun 2019 19:56:06: 33000000 INFO @ Sun, 02 Jun 2019 19:56:12: 37000000 INFO @ Sun, 02 Jun 2019 19:56:13: 38000000 INFO @ Sun, 02 Jun 2019 19:56:16: 34000000 INFO @ Sun, 02 Jun 2019 19:56:21: 38000000 INFO @ Sun, 02 Jun 2019 19:56:21: 39000000 INFO @ Sun, 02 Jun 2019 19:56:26: 35000000 INFO @ Sun, 02 Jun 2019 19:56:29: 39000000 INFO @ Sun, 02 Jun 2019 19:56:30: 40000000 INFO @ Sun, 02 Jun 2019 19:56:35: 36000000 INFO @ Sun, 02 Jun 2019 19:56:38: 40000000 INFO @ Sun, 02 Jun 2019 19:56:39: 41000000 INFO @ Sun, 02 Jun 2019 19:56:43: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:56:43: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:56:43: #1 total tags in treatment: 19143810 INFO @ Sun, 02 Jun 2019 19:56:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:56:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:56:44: #1 tags after filtering in treatment: 15929410 INFO @ Sun, 02 Jun 2019 19:56:44: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 19:56:44: #1 finished! INFO @ Sun, 02 Jun 2019 19:56:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:56:45: 37000000 INFO @ Sun, 02 Jun 2019 19:56:45: #2 number of paired peaks: 815 WARNING @ Sun, 02 Jun 2019 19:56:45: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Sun, 02 Jun 2019 19:56:45: start model_add_line... INFO @ Sun, 02 Jun 2019 19:56:46: start X-correlation... INFO @ Sun, 02 Jun 2019 19:56:46: end of X-cor INFO @ Sun, 02 Jun 2019 19:56:46: #2 finished! INFO @ Sun, 02 Jun 2019 19:56:46: #2 predicted fragment length is 214 bps INFO @ Sun, 02 Jun 2019 19:56:46: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 02 Jun 2019 19:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.05_model.r INFO @ Sun, 02 Jun 2019 19:56:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:56:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:56:47: 41000000 INFO @ Sun, 02 Jun 2019 19:56:51: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:56:51: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:56:51: #1 total tags in treatment: 19143810 INFO @ Sun, 02 Jun 2019 19:56:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:56:52: #1 tags after filtering in treatment: 15929410 INFO @ Sun, 02 Jun 2019 19:56:52: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 19:56:52: #1 finished! INFO @ Sun, 02 Jun 2019 19:56:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:56:53: #2 number of paired peaks: 815 WARNING @ Sun, 02 Jun 2019 19:56:53: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Sun, 02 Jun 2019 19:56:53: start model_add_line... INFO @ Sun, 02 Jun 2019 19:56:53: start X-correlation... INFO @ Sun, 02 Jun 2019 19:56:53: end of X-cor INFO @ Sun, 02 Jun 2019 19:56:53: #2 finished! INFO @ Sun, 02 Jun 2019 19:56:53: #2 predicted fragment length is 214 bps INFO @ Sun, 02 Jun 2019 19:56:53: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 02 Jun 2019 19:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.10_model.r INFO @ Sun, 02 Jun 2019 19:56:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:56:54: 38000000 INFO @ Sun, 02 Jun 2019 19:57:04: 39000000 INFO @ Sun, 02 Jun 2019 19:57:13: 40000000 INFO @ Sun, 02 Jun 2019 19:57:23: 41000000 INFO @ Sun, 02 Jun 2019 19:57:28: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:57:28: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:57:28: #1 total tags in treatment: 19143810 INFO @ Sun, 02 Jun 2019 19:57:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:57:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:57:28: #1 tags after filtering in treatment: 15929410 INFO @ Sun, 02 Jun 2019 19:57:28: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 19:57:28: #1 finished! INFO @ Sun, 02 Jun 2019 19:57:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:57:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:57:30: #2 number of paired peaks: 815 WARNING @ Sun, 02 Jun 2019 19:57:30: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Sun, 02 Jun 2019 19:57:30: start model_add_line... INFO @ Sun, 02 Jun 2019 19:57:30: start X-correlation... INFO @ Sun, 02 Jun 2019 19:57:30: end of X-cor INFO @ Sun, 02 Jun 2019 19:57:30: #2 finished! INFO @ Sun, 02 Jun 2019 19:57:30: #2 predicted fragment length is 214 bps INFO @ Sun, 02 Jun 2019 19:57:30: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 02 Jun 2019 19:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.20_model.r INFO @ Sun, 02 Jun 2019 19:57:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:57:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:57:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:57:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.05_summits.bed INFO @ Sun, 02 Jun 2019 19:57:55: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (4775 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.10_summits.bed INFO @ Sun, 02 Jun 2019 19:58:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2873 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:58:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:58:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:58:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:58:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733152/SRX3733152.20_summits.bed INFO @ Sun, 02 Jun 2019 19:58:39: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1413 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。