Job ID = 1299275 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:13:42 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 ) 2019-06-03T09:13:42 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 ) 2019-06-03T09:18:04 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 : 15,940,109 reads read : 31,880,218 reads written : 31,880,218 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: 00:00:01 Multiseed full-index search: 00:31:04 15940109 reads; of these: 15940109 (100.00%) were paired; of these: 910373 (5.71%) aligned concordantly 0 times 12166183 (76.32%) aligned concordantly exactly 1 time 2863553 (17.96%) aligned concordantly >1 times ---- 910373 pairs aligned concordantly 0 times; of these: 105125 (11.55%) aligned discordantly 1 time ---- 805248 pairs aligned 0 times concordantly or discordantly; of these: 1610496 mates make up the pairs; of these: 1178407 (73.17%) aligned 0 times 330748 (20.54%) aligned exactly 1 time 101341 (6.29%) aligned >1 times 96.30% overall alignment rate Time searching: 00:31:05 Overall time: 00:31:05 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 16 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] 1384160 / 15123142 = 0.0915 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 19:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.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 19:01:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:01:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.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 19:01:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:01:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.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 19:01:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:01:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:01:12: 1000000 INFO @ Mon, 03 Jun 2019 19:01:12: 1000000 INFO @ Mon, 03 Jun 2019 19:01:12: 1000000 INFO @ Mon, 03 Jun 2019 19:01:20: 2000000 INFO @ Mon, 03 Jun 2019 19:01:20: 2000000 INFO @ Mon, 03 Jun 2019 19:01:20: 2000000 INFO @ Mon, 03 Jun 2019 19:01:28: 3000000 INFO @ Mon, 03 Jun 2019 19:01:28: 3000000 INFO @ Mon, 03 Jun 2019 19:01:28: 3000000 INFO @ Mon, 03 Jun 2019 19:01:36: 4000000 INFO @ Mon, 03 Jun 2019 19:01:36: 4000000 INFO @ Mon, 03 Jun 2019 19:01:36: 4000000 INFO @ Mon, 03 Jun 2019 19:01:44: 5000000 INFO @ Mon, 03 Jun 2019 19:01:44: 5000000 INFO @ Mon, 03 Jun 2019 19:01:44: 5000000 INFO @ Mon, 03 Jun 2019 19:01:52: 6000000 INFO @ Mon, 03 Jun 2019 19:01:52: 6000000 INFO @ Mon, 03 Jun 2019 19:01:52: 6000000 INFO @ Mon, 03 Jun 2019 19:02:00: 7000000 INFO @ Mon, 03 Jun 2019 19:02:00: 7000000 INFO @ Mon, 03 Jun 2019 19:02:00: 7000000 INFO @ Mon, 03 Jun 2019 19:02:07: 8000000 INFO @ Mon, 03 Jun 2019 19:02:07: 8000000 INFO @ Mon, 03 Jun 2019 19:02:08: 8000000 INFO @ Mon, 03 Jun 2019 19:02:14: 9000000 INFO @ Mon, 03 Jun 2019 19:02:14: 9000000 INFO @ Mon, 03 Jun 2019 19:02:15: 9000000 INFO @ Mon, 03 Jun 2019 19:02:21: 10000000 INFO @ Mon, 03 Jun 2019 19:02:21: 10000000 INFO @ Mon, 03 Jun 2019 19:02:23: 10000000 INFO @ Mon, 03 Jun 2019 19:02:28: 11000000 INFO @ Mon, 03 Jun 2019 19:02:28: 11000000 INFO @ Mon, 03 Jun 2019 19:02:30: 11000000 INFO @ Mon, 03 Jun 2019 19:02:35: 12000000 INFO @ Mon, 03 Jun 2019 19:02:35: 12000000 INFO @ Mon, 03 Jun 2019 19:02:38: 12000000 INFO @ Mon, 03 Jun 2019 19:02:43: 13000000 INFO @ Mon, 03 Jun 2019 19:02:44: 13000000 INFO @ Mon, 03 Jun 2019 19:02:47: 13000000 INFO @ Mon, 03 Jun 2019 19:02:53: 14000000 INFO @ Mon, 03 Jun 2019 19:02:53: 14000000 INFO @ Mon, 03 Jun 2019 19:02:56: 14000000 INFO @ Mon, 03 Jun 2019 19:03:02: 15000000 INFO @ Mon, 03 Jun 2019 19:03:02: 15000000 INFO @ Mon, 03 Jun 2019 19:03:04: 15000000 INFO @ Mon, 03 Jun 2019 19:03:10: 16000000 INFO @ Mon, 03 Jun 2019 19:03:11: 16000000 INFO @ Mon, 03 Jun 2019 19:03:13: 16000000 INFO @ Mon, 03 Jun 2019 19:03:17: 17000000 INFO @ Mon, 03 Jun 2019 19:03:17: 17000000 INFO @ Mon, 03 Jun 2019 19:03:20: 17000000 INFO @ Mon, 03 Jun 2019 19:03:24: 18000000 INFO @ Mon, 03 Jun 2019 19:03:24: 18000000 INFO @ Mon, 03 Jun 2019 19:03:27: 18000000 INFO @ Mon, 03 Jun 2019 19:03:31: 19000000 INFO @ Mon, 03 Jun 2019 19:03:31: 19000000 INFO @ Mon, 03 Jun 2019 19:03:35: 19000000 INFO @ Mon, 03 Jun 2019 19:03:38: 20000000 INFO @ Mon, 03 Jun 2019 19:03:38: 20000000 INFO @ Mon, 03 Jun 2019 19:03:43: 20000000 INFO @ Mon, 03 Jun 2019 19:03:45: 21000000 INFO @ Mon, 03 Jun 2019 19:03:45: 21000000 INFO @ Mon, 03 Jun 2019 19:03:51: 21000000 INFO @ Mon, 03 Jun 2019 19:03:52: 22000000 INFO @ Mon, 03 Jun 2019 19:03:52: 22000000 INFO @ Mon, 03 Jun 2019 19:03:59: 22000000 INFO @ Mon, 03 Jun 2019 19:03:59: 23000000 INFO @ Mon, 03 Jun 2019 19:03:59: 23000000 INFO @ Mon, 03 Jun 2019 19:04:06: 24000000 INFO @ Mon, 03 Jun 2019 19:04:06: 24000000 INFO @ Mon, 03 Jun 2019 19:04:07: 23000000 INFO @ Mon, 03 Jun 2019 19:04:13: 25000000 INFO @ Mon, 03 Jun 2019 19:04:13: 25000000 INFO @ Mon, 03 Jun 2019 19:04:14: 24000000 INFO @ Mon, 03 Jun 2019 19:04:20: 26000000 INFO @ Mon, 03 Jun 2019 19:04:20: 26000000 INFO @ Mon, 03 Jun 2019 19:04:22: 25000000 INFO @ Mon, 03 Jun 2019 19:04:26: 27000000 INFO @ Mon, 03 Jun 2019 19:04:27: 27000000 INFO @ Mon, 03 Jun 2019 19:04:30: 26000000 INFO @ Mon, 03 Jun 2019 19:04:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:04:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:04:33: #1 total tags in treatment: 13648939 INFO @ Mon, 03 Jun 2019 19:04:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:04:33: #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 19:04:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:04:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:04:33: #1 total tags in treatment: 13648939 INFO @ Mon, 03 Jun 2019 19:04:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:04:33: #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 19:04:33: #1 tags after filtering in treatment: 12026849 INFO @ Mon, 03 Jun 2019 19:04:33: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:04:33: #1 finished! INFO @ Mon, 03 Jun 2019 19:04:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:04:33: #1 tags after filtering in treatment: 12026849 INFO @ Mon, 03 Jun 2019 19:04:33: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:04:33: #1 finished! INFO @ Mon, 03 Jun 2019 19:04:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:04:34: #2 number of paired peaks: 13 WARNING @ Mon, 03 Jun 2019 19:04:34: Too few paired peaks (13) 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 19:04:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.10_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/SRX474572/SRX474572.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:04:35: #2 number of paired peaks: 13 WARNING @ Mon, 03 Jun 2019 19:04:35: Too few paired peaks (13) 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 19:04:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.05_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/SRX474572/SRX474572.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:04:38: 27000000 INFO @ Mon, 03 Jun 2019 19:04:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:04:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:04:45: #1 total tags in treatment: 13648939 INFO @ Mon, 03 Jun 2019 19:04:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:04:45: #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 19:04:46: #1 tags after filtering in treatment: 12026849 INFO @ Mon, 03 Jun 2019 19:04:46: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:04:46: #1 finished! INFO @ Mon, 03 Jun 2019 19:04:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:04:47: #2 number of paired peaks: 13 WARNING @ Mon, 03 Jun 2019 19:04:47: Too few paired peaks (13) 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 19:04:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.20_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/SRX474572/SRX474572.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX474572/SRX474572.20_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。