Job ID = 2640996 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:18:50 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 ) 2019-08-24T11:18:50 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 ) 2019-08-24T11:18:50 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 : 11,689,186 reads read : 23,378,372 reads written : 23,378,372 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: 00:14:51 11689186 reads; of these: 11689186 (100.00%) were paired; of these: 669480 (5.73%) aligned concordantly 0 times 10167188 (86.98%) aligned concordantly exactly 1 time 852518 (7.29%) aligned concordantly >1 times ---- 669480 pairs aligned concordantly 0 times; of these: 86071 (12.86%) aligned discordantly 1 time ---- 583409 pairs aligned 0 times concordantly or discordantly; of these: 1166818 mates make up the pairs; of these: 1124726 (96.39%) aligned 0 times 24056 (2.06%) aligned exactly 1 time 18036 (1.55%) aligned >1 times 95.19% overall alignment rate Time searching: 00:14:51 Overall time: 00:14:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 130123 / 11101659 = 0.0117 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 21:01:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:01:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:01:32: 1000000 INFO @ Sat, 24 Aug 2019 21:01:41: 2000000 INFO @ Sat, 24 Aug 2019 21:01:51: 3000000 INFO @ Sat, 24 Aug 2019 21:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 21:01:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:01:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:01: 4000000 INFO @ Sat, 24 Aug 2019 21:02:05: 1000000 INFO @ Sat, 24 Aug 2019 21:02:11: 5000000 INFO @ Sat, 24 Aug 2019 21:02:17: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:02:21: 6000000 INFO @ Sat, 24 Aug 2019 21:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 21:02:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:02:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:31: 7000000 INFO @ Sat, 24 Aug 2019 21:02:32: 3000000 INFO @ Sat, 24 Aug 2019 21:02:38: 1000000 INFO @ Sat, 24 Aug 2019 21:02:41: 8000000 INFO @ Sat, 24 Aug 2019 21:02:48: 4000000 INFO @ Sat, 24 Aug 2019 21:02:51: 9000000 INFO @ Sat, 24 Aug 2019 21:02:53: 2000000 INFO @ Sat, 24 Aug 2019 21:03:01: 10000000 INFO @ Sat, 24 Aug 2019 21:03:03: 5000000 INFO @ Sat, 24 Aug 2019 21:03:09: 3000000 INFO @ Sat, 24 Aug 2019 21:03:11: 11000000 INFO @ Sat, 24 Aug 2019 21:03:18: 6000000 INFO @ Sat, 24 Aug 2019 21:03:21: 12000000 INFO @ Sat, 24 Aug 2019 21:03:24: 4000000 INFO @ Sat, 24 Aug 2019 21:03:31: 13000000 INFO @ Sat, 24 Aug 2019 21:03:34: 7000000 INFO @ Sat, 24 Aug 2019 21:03:39: 5000000 INFO @ Sat, 24 Aug 2019 21:03:42: 14000000 INFO @ Sat, 24 Aug 2019 21:03:49: 8000000 INFO @ Sat, 24 Aug 2019 21:03:52: 15000000 INFO @ Sat, 24 Aug 2019 21:03:55: 6000000 INFO @ Sat, 24 Aug 2019 21:04:02: 16000000 INFO @ Sat, 24 Aug 2019 21:04:04: 9000000 INFO @ Sat, 24 Aug 2019 21:04:10: 7000000 INFO @ Sat, 24 Aug 2019 21:04:12: 17000000 INFO @ Sat, 24 Aug 2019 21:04:20: 10000000 INFO @ Sat, 24 Aug 2019 21:04:21: 18000000 INFO @ Sat, 24 Aug 2019 21:04:25: 8000000 INFO @ Sat, 24 Aug 2019 21:04:31: 19000000 INFO @ Sat, 24 Aug 2019 21:04:35: 11000000 INFO @ Sat, 24 Aug 2019 21:04:41: 9000000 INFO @ Sat, 24 Aug 2019 21:04:41: 20000000 INFO @ Sat, 24 Aug 2019 21:04:50: 12000000 INFO @ Sat, 24 Aug 2019 21:04:51: 21000000 INFO @ Sat, 24 Aug 2019 21:04:56: 10000000 INFO @ Sat, 24 Aug 2019 21:05:01: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:05:01: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:05:01: #1 total tags in treatment: 10890136 INFO @ Sat, 24 Aug 2019 21:05:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:05:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:05:01: #1 tags after filtering in treatment: 7794223 INFO @ Sat, 24 Aug 2019 21:05:01: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:05:01: #1 finished! INFO @ Sat, 24 Aug 2019 21:05:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:05:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:05:02: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:05:02: 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 @ Sat, 24 Aug 2019 21:05:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.05_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/sacCer3/SRX4936102/SRX4936102.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:05:06: 13000000 INFO @ Sat, 24 Aug 2019 21:05:11: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:05:21: 14000000 INFO @ Sat, 24 Aug 2019 21:05:26: 12000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:05:36: 15000000 INFO @ Sat, 24 Aug 2019 21:05:41: 13000000 INFO @ Sat, 24 Aug 2019 21:05:51: 16000000 INFO @ Sat, 24 Aug 2019 21:05:56: 14000000 INFO @ Sat, 24 Aug 2019 21:06:06: 17000000 INFO @ Sat, 24 Aug 2019 21:06:11: 15000000 INFO @ Sat, 24 Aug 2019 21:06:20: 18000000 INFO @ Sat, 24 Aug 2019 21:06:26: 16000000 INFO @ Sat, 24 Aug 2019 21:06:35: 19000000 INFO @ Sat, 24 Aug 2019 21:06:41: 17000000 INFO @ Sat, 24 Aug 2019 21:06:50: 20000000 INFO @ Sat, 24 Aug 2019 21:06:56: 18000000 INFO @ Sat, 24 Aug 2019 21:07:05: 21000000 INFO @ Sat, 24 Aug 2019 21:07:10: 19000000 INFO @ Sat, 24 Aug 2019 21:07:19: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:07:19: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:07:19: #1 total tags in treatment: 10890136 INFO @ Sat, 24 Aug 2019 21:07:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:07:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:07:20: #1 tags after filtering in treatment: 7794223 INFO @ Sat, 24 Aug 2019 21:07:20: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:07:20: #1 finished! INFO @ Sat, 24 Aug 2019 21:07:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:07:20: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:07:20: 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 @ Sat, 24 Aug 2019 21:07:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.10_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/sacCer3/SRX4936102/SRX4936102.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:07:24: 20000000 INFO @ Sat, 24 Aug 2019 21:07:36: 21000000 INFO @ Sat, 24 Aug 2019 21:07:47: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:07:47: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:07:47: #1 total tags in treatment: 10890136 INFO @ Sat, 24 Aug 2019 21:07:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:07:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:07:48: #1 tags after filtering in treatment: 7794223 INFO @ Sat, 24 Aug 2019 21:07:48: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:07:48: #1 finished! INFO @ Sat, 24 Aug 2019 21:07:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:07:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:07:48: 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 @ Sat, 24 Aug 2019 21:07:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.20_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/sacCer3/SRX4936102/SRX4936102.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936102/SRX4936102.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling