Job ID = 1295824 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T06:40:42 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T06:40:42 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1153274/SRR1153274.1' 2019-06-03T06:40:42 fasterq-dump.2.9.6 err: invalid accession 'SRR1153274' spots read : 109,944,906 reads read : 109,944,906 reads written : 109,944,906 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:39:49 109944906 reads; of these: 109944906 (100.00%) were unpaired; of these: 5584664 (5.08%) aligned 0 times 80689673 (73.39%) aligned exactly 1 time 23670569 (21.53%) aligned >1 times 94.92% overall alignment rate Time searching: 00:39:50 Overall time: 00:39:50 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 44 files... [bam_rmdupse_core] 52296843 / 104360242 = 0.5011 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 16:56:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.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 16:56:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:56:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:56:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.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 16:56:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:56:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:56:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.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 16:56:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:56:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:56:43: 1000000 INFO @ Mon, 03 Jun 2019 16:56:44: 1000000 INFO @ Mon, 03 Jun 2019 16:56:46: 1000000 INFO @ Mon, 03 Jun 2019 16:56:51: 2000000 INFO @ Mon, 03 Jun 2019 16:56:53: 2000000 INFO @ Mon, 03 Jun 2019 16:56:56: 2000000 INFO @ Mon, 03 Jun 2019 16:56:59: 3000000 INFO @ Mon, 03 Jun 2019 16:57:01: 3000000 INFO @ Mon, 03 Jun 2019 16:57:06: 3000000 INFO @ Mon, 03 Jun 2019 16:57:08: 4000000 INFO @ Mon, 03 Jun 2019 16:57:09: 4000000 INFO @ Mon, 03 Jun 2019 16:57:16: 5000000 INFO @ Mon, 03 Jun 2019 16:57:16: 4000000 INFO @ Mon, 03 Jun 2019 16:57:18: 5000000 INFO @ Mon, 03 Jun 2019 16:57:24: 6000000 INFO @ Mon, 03 Jun 2019 16:57:26: 5000000 INFO @ Mon, 03 Jun 2019 16:57:27: 6000000 INFO @ Mon, 03 Jun 2019 16:57:32: 7000000 INFO @ Mon, 03 Jun 2019 16:57:35: 7000000 INFO @ Mon, 03 Jun 2019 16:57:36: 6000000 INFO @ Mon, 03 Jun 2019 16:57:40: 8000000 INFO @ Mon, 03 Jun 2019 16:57:44: 8000000 INFO @ Mon, 03 Jun 2019 16:57:47: 7000000 INFO @ Mon, 03 Jun 2019 16:57:51: 9000000 INFO @ Mon, 03 Jun 2019 16:57:54: 9000000 INFO @ Mon, 03 Jun 2019 16:57:58: 8000000 INFO @ Mon, 03 Jun 2019 16:57:59: 10000000 INFO @ Mon, 03 Jun 2019 16:58:03: 10000000 INFO @ Mon, 03 Jun 2019 16:58:07: 11000000 INFO @ Mon, 03 Jun 2019 16:58:08: 9000000 INFO @ Mon, 03 Jun 2019 16:58:11: 11000000 INFO @ Mon, 03 Jun 2019 16:58:15: 12000000 INFO @ Mon, 03 Jun 2019 16:58:19: 10000000 INFO @ Mon, 03 Jun 2019 16:58:20: 12000000 INFO @ Mon, 03 Jun 2019 16:58:23: 13000000 INFO @ Mon, 03 Jun 2019 16:58:28: 13000000 INFO @ Mon, 03 Jun 2019 16:58:29: 11000000 INFO @ Mon, 03 Jun 2019 16:58:31: 14000000 INFO @ Mon, 03 Jun 2019 16:58:37: 14000000 INFO @ Mon, 03 Jun 2019 16:58:39: 12000000 INFO @ Mon, 03 Jun 2019 16:58:39: 15000000 INFO @ Mon, 03 Jun 2019 16:58:46: 15000000 INFO @ Mon, 03 Jun 2019 16:58:47: 16000000 INFO @ Mon, 03 Jun 2019 16:58:49: 13000000 INFO @ Mon, 03 Jun 2019 16:58:54: 16000000 INFO @ Mon, 03 Jun 2019 16:58:56: 17000000 INFO @ Mon, 03 Jun 2019 16:58:59: 14000000 INFO @ Mon, 03 Jun 2019 16:59:03: 17000000 INFO @ Mon, 03 Jun 2019 16:59:03: 18000000 INFO @ Mon, 03 Jun 2019 16:59:10: 15000000 INFO @ Mon, 03 Jun 2019 16:59:11: 19000000 INFO @ Mon, 03 Jun 2019 16:59:11: 18000000 INFO @ Mon, 03 Jun 2019 16:59:19: 20000000 INFO @ Mon, 03 Jun 2019 16:59:20: 19000000 INFO @ Mon, 03 Jun 2019 16:59:20: 16000000 INFO @ Mon, 03 Jun 2019 16:59:29: 21000000 INFO @ Mon, 03 Jun 2019 16:59:29: 20000000 INFO @ Mon, 03 Jun 2019 16:59:30: 17000000 INFO @ Mon, 03 Jun 2019 16:59:37: 22000000 INFO @ Mon, 03 Jun 2019 16:59:37: 21000000 INFO @ Mon, 03 Jun 2019 16:59:40: 18000000 INFO @ Mon, 03 Jun 2019 16:59:45: 23000000 INFO @ Mon, 03 Jun 2019 16:59:46: 22000000 INFO @ Mon, 03 Jun 2019 16:59:50: 19000000 INFO @ Mon, 03 Jun 2019 16:59:53: 24000000 INFO @ Mon, 03 Jun 2019 16:59:54: 23000000 INFO @ Mon, 03 Jun 2019 17:00:00: 20000000 INFO @ Mon, 03 Jun 2019 17:00:00: 25000000 INFO @ Mon, 03 Jun 2019 17:00:04: 24000000 INFO @ Mon, 03 Jun 2019 17:00:08: 26000000 INFO @ Mon, 03 Jun 2019 17:00:10: 21000000 INFO @ Mon, 03 Jun 2019 17:00:13: 25000000 INFO @ Mon, 03 Jun 2019 17:00:16: 27000000 INFO @ Mon, 03 Jun 2019 17:00:20: 22000000 INFO @ Mon, 03 Jun 2019 17:00:22: 26000000 INFO @ Mon, 03 Jun 2019 17:00:24: 28000000 INFO @ Mon, 03 Jun 2019 17:00:31: 23000000 INFO @ Mon, 03 Jun 2019 17:00:31: 27000000 INFO @ Mon, 03 Jun 2019 17:00:32: 29000000 INFO @ Mon, 03 Jun 2019 17:00:40: 30000000 INFO @ Mon, 03 Jun 2019 17:00:40: 28000000 INFO @ Mon, 03 Jun 2019 17:00:41: 24000000 INFO @ Mon, 03 Jun 2019 17:00:47: 31000000 INFO @ Mon, 03 Jun 2019 17:00:48: 29000000 INFO @ Mon, 03 Jun 2019 17:00:51: 25000000 INFO @ Mon, 03 Jun 2019 17:00:55: 32000000 INFO @ Mon, 03 Jun 2019 17:00:57: 30000000 INFO @ Mon, 03 Jun 2019 17:01:01: 26000000 INFO @ Mon, 03 Jun 2019 17:01:03: 33000000 INFO @ Mon, 03 Jun 2019 17:01:06: 31000000 INFO @ Mon, 03 Jun 2019 17:01:11: 27000000 INFO @ Mon, 03 Jun 2019 17:01:11: 34000000 INFO @ Mon, 03 Jun 2019 17:01:15: 32000000 INFO @ Mon, 03 Jun 2019 17:01:19: 35000000 INFO @ Mon, 03 Jun 2019 17:01:21: 28000000 INFO @ Mon, 03 Jun 2019 17:01:23: 33000000 INFO @ Mon, 03 Jun 2019 17:01:27: 36000000 INFO @ Mon, 03 Jun 2019 17:01:31: 29000000 INFO @ Mon, 03 Jun 2019 17:01:31: 34000000 INFO @ Mon, 03 Jun 2019 17:01:35: 37000000 INFO @ Mon, 03 Jun 2019 17:01:41: 35000000 INFO @ Mon, 03 Jun 2019 17:01:41: 30000000 INFO @ Mon, 03 Jun 2019 17:01:43: 38000000 INFO @ Mon, 03 Jun 2019 17:01:50: 36000000 INFO @ Mon, 03 Jun 2019 17:01:51: 39000000 INFO @ Mon, 03 Jun 2019 17:01:51: 31000000 INFO @ Mon, 03 Jun 2019 17:01:58: 37000000 INFO @ Mon, 03 Jun 2019 17:01:58: 40000000 INFO @ Mon, 03 Jun 2019 17:02:01: 32000000 INFO @ Mon, 03 Jun 2019 17:02:06: 41000000 INFO @ Mon, 03 Jun 2019 17:02:07: 38000000 INFO @ Mon, 03 Jun 2019 17:02:11: 33000000 INFO @ Mon, 03 Jun 2019 17:02:14: 42000000 INFO @ Mon, 03 Jun 2019 17:02:15: 39000000 INFO @ Mon, 03 Jun 2019 17:02:21: 34000000 INFO @ Mon, 03 Jun 2019 17:02:21: 43000000 INFO @ Mon, 03 Jun 2019 17:02:24: 40000000 INFO @ Mon, 03 Jun 2019 17:02:29: 44000000 INFO @ Mon, 03 Jun 2019 17:02:31: 35000000 INFO @ Mon, 03 Jun 2019 17:02:33: 41000000 INFO @ Mon, 03 Jun 2019 17:02:36: 45000000 INFO @ Mon, 03 Jun 2019 17:02:41: 36000000 INFO @ Mon, 03 Jun 2019 17:02:42: 42000000 INFO @ Mon, 03 Jun 2019 17:02:44: 46000000 INFO @ Mon, 03 Jun 2019 17:02:50: 43000000 INFO @ Mon, 03 Jun 2019 17:02:51: 37000000 INFO @ Mon, 03 Jun 2019 17:02:51: 47000000 INFO @ Mon, 03 Jun 2019 17:02:59: 44000000 INFO @ Mon, 03 Jun 2019 17:02:59: 48000000 INFO @ Mon, 03 Jun 2019 17:03:01: 38000000 INFO @ Mon, 03 Jun 2019 17:03:07: 49000000 INFO @ Mon, 03 Jun 2019 17:03:07: 45000000 INFO @ Mon, 03 Jun 2019 17:03:11: 39000000 INFO @ Mon, 03 Jun 2019 17:03:14: 50000000 INFO @ Mon, 03 Jun 2019 17:03:16: 46000000 INFO @ Mon, 03 Jun 2019 17:03:21: 40000000 INFO @ Mon, 03 Jun 2019 17:03:22: 51000000 INFO @ Mon, 03 Jun 2019 17:03:25: 47000000 INFO @ Mon, 03 Jun 2019 17:03:29: 52000000 INFO @ Mon, 03 Jun 2019 17:03:30: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 17:03:30: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 17:03:30: #1 total tags in treatment: 52063399 INFO @ Mon, 03 Jun 2019 17:03:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:03:30: #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 17:03:31: 41000000 INFO @ Mon, 03 Jun 2019 17:03:31: #1 tags after filtering in treatment: 52063399 INFO @ Mon, 03 Jun 2019 17:03:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:03:31: #1 finished! INFO @ Mon, 03 Jun 2019 17:03:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:03:34: 48000000 INFO @ Mon, 03 Jun 2019 17:03:36: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 17:03:36: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 03 Jun 2019 17:03:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:03:41: 42000000 INFO @ Mon, 03 Jun 2019 17:03:43: 49000000 INFO @ Mon, 03 Jun 2019 17:03:51: 43000000 INFO @ Mon, 03 Jun 2019 17:03:52: 50000000 INFO @ Mon, 03 Jun 2019 17:04:00: 51000000 INFO @ Mon, 03 Jun 2019 17:04:01: 44000000 INFO @ Mon, 03 Jun 2019 17:04:09: 52000000 INFO @ Mon, 03 Jun 2019 17:04:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 17:04:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 17:04:10: #1 total tags in treatment: 52063399 INFO @ Mon, 03 Jun 2019 17:04:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:04:10: #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 17:04:10: 45000000 INFO @ Mon, 03 Jun 2019 17:04:11: #1 tags after filtering in treatment: 52063399 INFO @ Mon, 03 Jun 2019 17:04:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:04:11: #1 finished! INFO @ Mon, 03 Jun 2019 17:04:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:04:15: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 17:04:15: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 03 Jun 2019 17:04:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:04:20: 46000000 INFO @ Mon, 03 Jun 2019 17:04:29: 47000000 INFO @ Mon, 03 Jun 2019 17:04:38: 48000000 INFO @ Mon, 03 Jun 2019 17:04:47: 49000000 INFO @ Mon, 03 Jun 2019 17:04:57: 50000000 INFO @ Mon, 03 Jun 2019 17:05:06: 51000000 INFO @ Mon, 03 Jun 2019 17:05:15: 52000000 INFO @ Mon, 03 Jun 2019 17:05:17: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 17:05:17: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 17:05:17: #1 total tags in treatment: 52063399 INFO @ Mon, 03 Jun 2019 17:05:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:05:17: #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 17:05:18: #1 tags after filtering in treatment: 52063399 INFO @ Mon, 03 Jun 2019 17:05:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:05:18: #1 finished! INFO @ Mon, 03 Jun 2019 17:05:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:05:22: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 17:05:22: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 03 Jun 2019 17:05:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX457598/SRX457598.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。