Job ID = 2640991 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:18:35 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 ) 2019-08-24T11:18:35 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 ) 2019-08-24T11:18:35 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 : 11,798,017 reads read : 23,596,034 reads written : 23,596,034 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: 00:00:01 Multiseed full-index search: 00:14:12 11798017 reads; of these: 11798017 (100.00%) were paired; of these: 761264 (6.45%) aligned concordantly 0 times 10016833 (84.90%) aligned concordantly exactly 1 time 1019920 (8.64%) aligned concordantly >1 times ---- 761264 pairs aligned concordantly 0 times; of these: 97156 (12.76%) aligned discordantly 1 time ---- 664108 pairs aligned 0 times concordantly or discordantly; of these: 1328216 mates make up the pairs; of these: 1274524 (95.96%) aligned 0 times 29460 (2.22%) aligned exactly 1 time 24232 (1.82%) aligned >1 times 94.60% overall alignment rate Time searching: 00:14:13 Overall time: 00:14:13 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] 120966 / 11130390 = 0.0109 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.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 20:59:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:59:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:59:17: 1000000 INFO @ Sat, 24 Aug 2019 20:59:27: 2000000 INFO @ Sat, 24 Aug 2019 20:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.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 20:59:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:59:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:59:37: 3000000 INFO @ Sat, 24 Aug 2019 20:59:46: 1000000 INFO @ Sat, 24 Aug 2019 20:59:48: 4000000 INFO @ Sat, 24 Aug 2019 20:59:55: 2000000 INFO @ Sat, 24 Aug 2019 20:59:58: 5000000 INFO @ Sat, 24 Aug 2019 21:00:04: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.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 21:00:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:00:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:00:09: 6000000 INFO @ Sat, 24 Aug 2019 21:00:13: 4000000 INFO @ Sat, 24 Aug 2019 21:00:20: 7000000 INFO @ Sat, 24 Aug 2019 21:00:21: 1000000 INFO @ Sat, 24 Aug 2019 21:00:22: 5000000 INFO @ Sat, 24 Aug 2019 21:00:30: 8000000 INFO @ Sat, 24 Aug 2019 21:00:32: 6000000 INFO @ Sat, 24 Aug 2019 21:00:35: 2000000 INFO @ Sat, 24 Aug 2019 21:00:41: 7000000 INFO @ Sat, 24 Aug 2019 21:00:41: 9000000 INFO @ Sat, 24 Aug 2019 21:00:48: 3000000 INFO @ Sat, 24 Aug 2019 21:00:50: 8000000 INFO @ Sat, 24 Aug 2019 21:00:52: 10000000 INFO @ Sat, 24 Aug 2019 21:00:59: 9000000 INFO @ Sat, 24 Aug 2019 21:01:02: 4000000 INFO @ Sat, 24 Aug 2019 21:01:03: 11000000 INFO @ Sat, 24 Aug 2019 21:01:09: 10000000 INFO @ Sat, 24 Aug 2019 21:01:13: 12000000 INFO @ Sat, 24 Aug 2019 21:01:16: 5000000 INFO @ Sat, 24 Aug 2019 21:01:18: 11000000 INFO @ Sat, 24 Aug 2019 21:01:24: 13000000 INFO @ Sat, 24 Aug 2019 21:01:28: 12000000 INFO @ Sat, 24 Aug 2019 21:01:29: 6000000 INFO @ Sat, 24 Aug 2019 21:01:35: 14000000 INFO @ Sat, 24 Aug 2019 21:01:39: 13000000 INFO @ Sat, 24 Aug 2019 21:01:43: 7000000 INFO @ Sat, 24 Aug 2019 21:01:47: 15000000 INFO @ Sat, 24 Aug 2019 21:01:49: 14000000 INFO @ Sat, 24 Aug 2019 21:01:57: 8000000 INFO @ Sat, 24 Aug 2019 21:01:57: 16000000 INFO @ Sat, 24 Aug 2019 21:01:59: 15000000 INFO @ Sat, 24 Aug 2019 21:02:08: 16000000 INFO @ Sat, 24 Aug 2019 21:02:08: 17000000 INFO @ Sat, 24 Aug 2019 21:02:11: 9000000 INFO @ Sat, 24 Aug 2019 21:02:17: 17000000 INFO @ Sat, 24 Aug 2019 21:02:19: 18000000 INFO @ Sat, 24 Aug 2019 21:02:24: 10000000 INFO @ Sat, 24 Aug 2019 21:02:26: 18000000 INFO @ Sat, 24 Aug 2019 21:02:29: 19000000 INFO @ Sat, 24 Aug 2019 21:02:36: 19000000 INFO @ Sat, 24 Aug 2019 21:02:38: 11000000 INFO @ Sat, 24 Aug 2019 21:02:40: 20000000 INFO @ Sat, 24 Aug 2019 21:02:45: 20000000 INFO @ Sat, 24 Aug 2019 21:02:51: 21000000 INFO @ Sat, 24 Aug 2019 21:02:51: 12000000 INFO @ Sat, 24 Aug 2019 21:02:54: 21000000 INFO @ Sat, 24 Aug 2019 21:03:02: 22000000 INFO @ Sat, 24 Aug 2019 21:03:03: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:03:03: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:03:03: #1 total tags in treatment: 10916334 INFO @ Sat, 24 Aug 2019 21:03:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:03:03: #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 21:03:03: #1 tags after filtering in treatment: 8142999 INFO @ Sat, 24 Aug 2019 21:03:03: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 24 Aug 2019 21:03:03: #1 finished! INFO @ Sat, 24 Aug 2019 21:03:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:03:03: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:03:03: 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 21:03:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.05_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/SRX4936097/SRX4936097.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:03:04: 22000000 INFO @ Sat, 24 Aug 2019 21:03:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:03:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:03:04: #1 total tags in treatment: 10916334 INFO @ Sat, 24 Aug 2019 21:03:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:03:04: #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 21:03:05: #1 tags after filtering in treatment: 8142999 INFO @ Sat, 24 Aug 2019 21:03:05: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 24 Aug 2019 21:03:05: #1 finished! INFO @ Sat, 24 Aug 2019 21:03:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:03:05: 13000000 INFO @ Sat, 24 Aug 2019 21:03:05: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:03:05: 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 21:03:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.10_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/SRX4936097/SRX4936097.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:03:18: 14000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:03:30: 15000000 INFO @ Sat, 24 Aug 2019 21:03:43: 16000000 INFO @ Sat, 24 Aug 2019 21:03:56: 17000000 INFO @ Sat, 24 Aug 2019 21:04:08: 18000000 INFO @ Sat, 24 Aug 2019 21:04:21: 19000000 INFO @ Sat, 24 Aug 2019 21:04:34: 20000000 INFO @ Sat, 24 Aug 2019 21:04:46: 21000000 INFO @ Sat, 24 Aug 2019 21:04:59: 22000000 INFO @ Sat, 24 Aug 2019 21:05:00: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:05:00: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:05:00: #1 total tags in treatment: 10916334 INFO @ Sat, 24 Aug 2019 21:05:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:05:00: #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 21:05:00: #1 tags after filtering in treatment: 8142999 INFO @ Sat, 24 Aug 2019 21:05:00: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 24 Aug 2019 21:05:00: #1 finished! INFO @ Sat, 24 Aug 2019 21:05:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:05:01: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:05:01: 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 21:05:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.20_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/sacCer3/SRX4936097/SRX4936097.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936097/SRX4936097.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling