Job ID = 2590964 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-12T15:09:12 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 ) 2019-08-12T15:09:12 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 ) 2019-08-12T15:09:12 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 : 21,983,204 reads read : 43,966,408 reads written : 43,966,408 rm: cannot remove ‘[DSE]RR*’: 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: 00:42:43 21983204 reads; of these: 21983204 (100.00%) were paired; of these: 2616647 (11.90%) aligned concordantly 0 times 15344468 (69.80%) aligned concordantly exactly 1 time 4022089 (18.30%) aligned concordantly >1 times ---- 2616647 pairs aligned concordantly 0 times; of these: 294704 (11.26%) aligned discordantly 1 time ---- 2321943 pairs aligned 0 times concordantly or discordantly; of these: 4643886 mates make up the pairs; of these: 3807766 (82.00%) aligned 0 times 551855 (11.88%) aligned exactly 1 time 284265 (6.12%) aligned >1 times 91.34% overall alignment rate Time searching: 00:42:43 Overall time: 00:42:43 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1450030 / 19608671 = 0.0739 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 @ Tue, 13 Aug 2019 01:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.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 @ Tue, 13 Aug 2019 01:23:27: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:23:27: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.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 @ Tue, 13 Aug 2019 01:23:27: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:23:27: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.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 @ Tue, 13 Aug 2019 01:23:28: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:23:28: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:23:34: 1000000 INFO @ Tue, 13 Aug 2019 01:23:34: 1000000 INFO @ Tue, 13 Aug 2019 01:23:37: 1000000 INFO @ Tue, 13 Aug 2019 01:23:41: 2000000 INFO @ Tue, 13 Aug 2019 01:23:42: 2000000 INFO @ Tue, 13 Aug 2019 01:23:46: 2000000 INFO @ Tue, 13 Aug 2019 01:23:48: 3000000 INFO @ Tue, 13 Aug 2019 01:23:49: 3000000 INFO @ Tue, 13 Aug 2019 01:23:54: 4000000 INFO @ Tue, 13 Aug 2019 01:23:54: 3000000 INFO @ Tue, 13 Aug 2019 01:23:57: 4000000 INFO @ Tue, 13 Aug 2019 01:24:01: 5000000 INFO @ Tue, 13 Aug 2019 01:24:03: 4000000 INFO @ Tue, 13 Aug 2019 01:24:04: 5000000 INFO @ Tue, 13 Aug 2019 01:24:08: 6000000 INFO @ Tue, 13 Aug 2019 01:24:12: 6000000 INFO @ Tue, 13 Aug 2019 01:24:12: 5000000 INFO @ Tue, 13 Aug 2019 01:24:14: 7000000 INFO @ Tue, 13 Aug 2019 01:24:19: 7000000 INFO @ Tue, 13 Aug 2019 01:24:21: 6000000 INFO @ Tue, 13 Aug 2019 01:24:21: 8000000 INFO @ Tue, 13 Aug 2019 01:24:27: 8000000 INFO @ Tue, 13 Aug 2019 01:24:28: 9000000 INFO @ Tue, 13 Aug 2019 01:24:29: 7000000 INFO @ Tue, 13 Aug 2019 01:24:34: 9000000 INFO @ Tue, 13 Aug 2019 01:24:34: 10000000 INFO @ Tue, 13 Aug 2019 01:24:38: 8000000 INFO @ Tue, 13 Aug 2019 01:24:41: 11000000 INFO @ Tue, 13 Aug 2019 01:24:42: 10000000 INFO @ Tue, 13 Aug 2019 01:24:47: 9000000 INFO @ Tue, 13 Aug 2019 01:24:48: 12000000 INFO @ Tue, 13 Aug 2019 01:24:49: 11000000 INFO @ Tue, 13 Aug 2019 01:24:54: 13000000 INFO @ Tue, 13 Aug 2019 01:24:55: 10000000 INFO @ Tue, 13 Aug 2019 01:24:56: 12000000 INFO @ Tue, 13 Aug 2019 01:25:01: 14000000 INFO @ Tue, 13 Aug 2019 01:25:04: 13000000 INFO @ Tue, 13 Aug 2019 01:25:04: 11000000 INFO @ Tue, 13 Aug 2019 01:25:07: 15000000 INFO @ Tue, 13 Aug 2019 01:25:11: 14000000 INFO @ Tue, 13 Aug 2019 01:25:13: 12000000 INFO @ Tue, 13 Aug 2019 01:25:14: 16000000 INFO @ Tue, 13 Aug 2019 01:25:19: 15000000 INFO @ Tue, 13 Aug 2019 01:25:21: 17000000 INFO @ Tue, 13 Aug 2019 01:25:22: 13000000 INFO @ Tue, 13 Aug 2019 01:25:26: 16000000 INFO @ Tue, 13 Aug 2019 01:25:27: 18000000 INFO @ Tue, 13 Aug 2019 01:25:30: 14000000 INFO @ Tue, 13 Aug 2019 01:25:34: 19000000 INFO @ Tue, 13 Aug 2019 01:25:34: 17000000 INFO @ Tue, 13 Aug 2019 01:25:39: 15000000 INFO @ Tue, 13 Aug 2019 01:25:41: 20000000 INFO @ Tue, 13 Aug 2019 01:25:42: 18000000 INFO @ Tue, 13 Aug 2019 01:25:47: 21000000 INFO @ Tue, 13 Aug 2019 01:25:48: 16000000 INFO @ Tue, 13 Aug 2019 01:25:49: 19000000 INFO @ Tue, 13 Aug 2019 01:25:54: 22000000 INFO @ Tue, 13 Aug 2019 01:25:57: 20000000 INFO @ Tue, 13 Aug 2019 01:25:57: 17000000 INFO @ Tue, 13 Aug 2019 01:26:01: 23000000 INFO @ Tue, 13 Aug 2019 01:26:04: 21000000 INFO @ Tue, 13 Aug 2019 01:26:06: 18000000 INFO @ Tue, 13 Aug 2019 01:26:07: 24000000 INFO @ Tue, 13 Aug 2019 01:26:11: 22000000 INFO @ Tue, 13 Aug 2019 01:26:14: 25000000 INFO @ Tue, 13 Aug 2019 01:26:14: 19000000 INFO @ Tue, 13 Aug 2019 01:26:19: 23000000 INFO @ Tue, 13 Aug 2019 01:26:21: 26000000 INFO @ Tue, 13 Aug 2019 01:26:23: 20000000 INFO @ Tue, 13 Aug 2019 01:26:26: 24000000 INFO @ Tue, 13 Aug 2019 01:26:27: 27000000 INFO @ Tue, 13 Aug 2019 01:26:32: 21000000 INFO @ Tue, 13 Aug 2019 01:26:34: 25000000 INFO @ Tue, 13 Aug 2019 01:26:34: 28000000 INFO @ Tue, 13 Aug 2019 01:26:40: 29000000 INFO @ Tue, 13 Aug 2019 01:26:41: 22000000 INFO @ Tue, 13 Aug 2019 01:26:41: 26000000 INFO @ Tue, 13 Aug 2019 01:26:47: 30000000 INFO @ Tue, 13 Aug 2019 01:26:48: 27000000 INFO @ Tue, 13 Aug 2019 01:26:49: 23000000 INFO @ Tue, 13 Aug 2019 01:26:54: 31000000 INFO @ Tue, 13 Aug 2019 01:26:55: 28000000 INFO @ Tue, 13 Aug 2019 01:26:58: 24000000 INFO @ Tue, 13 Aug 2019 01:27:00: 32000000 INFO @ Tue, 13 Aug 2019 01:27:03: 29000000 INFO @ Tue, 13 Aug 2019 01:27:07: 25000000 INFO @ Tue, 13 Aug 2019 01:27:07: 33000000 INFO @ Tue, 13 Aug 2019 01:27:10: 30000000 INFO @ Tue, 13 Aug 2019 01:27:14: 34000000 INFO @ Tue, 13 Aug 2019 01:27:15: 26000000 INFO @ Tue, 13 Aug 2019 01:27:18: 31000000 INFO @ Tue, 13 Aug 2019 01:27:20: 35000000 INFO @ Tue, 13 Aug 2019 01:27:24: 27000000 INFO @ Tue, 13 Aug 2019 01:27:25: 32000000 INFO @ Tue, 13 Aug 2019 01:27:27: 36000000 INFO @ Tue, 13 Aug 2019 01:27:32: 28000000 INFO @ Tue, 13 Aug 2019 01:27:33: 33000000 INFO @ Tue, 13 Aug 2019 01:27:33: 37000000 INFO @ Tue, 13 Aug 2019 01:27:35: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:27:35: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:27:35: #1 total tags in treatment: 17924490 INFO @ Tue, 13 Aug 2019 01:27:35: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:27:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:27:36: #1 tags after filtering in treatment: 14841231 INFO @ Tue, 13 Aug 2019 01:27:36: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:27:36: #1 finished! INFO @ Tue, 13 Aug 2019 01:27:36: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:27:37: #2 number of paired peaks: 14 WARNING @ Tue, 13 Aug 2019 01:27:37: Too few paired peaks (14) 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 @ Tue, 13 Aug 2019 01:27:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.10_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/SRX5865780/SRX5865780.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:27:40: 34000000 INFO @ Tue, 13 Aug 2019 01:27:41: 29000000 INFO @ Tue, 13 Aug 2019 01:27:47: 35000000 INFO @ Tue, 13 Aug 2019 01:27:50: 30000000 INFO @ Tue, 13 Aug 2019 01:27:55: 36000000 INFO @ Tue, 13 Aug 2019 01:27:58: 31000000 INFO @ Tue, 13 Aug 2019 01:28:02: 37000000 INFO @ Tue, 13 Aug 2019 01:28:04: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:28:04: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:28:04: #1 total tags in treatment: 17924490 INFO @ Tue, 13 Aug 2019 01:28:04: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:28:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:28:04: #1 tags after filtering in treatment: 14841231 INFO @ Tue, 13 Aug 2019 01:28:04: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:28:04: #1 finished! INFO @ Tue, 13 Aug 2019 01:28:04: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:28:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:28:06: #2 number of paired peaks: 14 WARNING @ Tue, 13 Aug 2019 01:28:06: Too few paired peaks (14) 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 @ Tue, 13 Aug 2019 01:28:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.05_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/SRX5865780/SRX5865780.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:28:07: 32000000 INFO @ Tue, 13 Aug 2019 01:28:15: 33000000 INFO @ Tue, 13 Aug 2019 01:28:24: 34000000 INFO @ Tue, 13 Aug 2019 01:28:32: 35000000 INFO @ Tue, 13 Aug 2019 01:28:40: 36000000 INFO @ Tue, 13 Aug 2019 01:28:49: 37000000 INFO @ Tue, 13 Aug 2019 01:28:51: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:28:51: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:28:51: #1 total tags in treatment: 17924490 INFO @ Tue, 13 Aug 2019 01:28:51: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:28:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:28:52: #1 tags after filtering in treatment: 14841231 INFO @ Tue, 13 Aug 2019 01:28:52: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:28:52: #1 finished! INFO @ Tue, 13 Aug 2019 01:28:52: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:28:53: #2 number of paired peaks: 14 WARNING @ Tue, 13 Aug 2019 01:28:53: Too few paired peaks (14) 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 @ Tue, 13 Aug 2019 01:28:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.20_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/SRX5865780/SRX5865780.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5865780/SRX5865780.20_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。