Job ID = 4289521 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-10T05:37:38 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T05:38:11 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 ) 2019-12-10T05:38:11 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 : 13,917,613 reads read : 27,835,226 reads written : 27,835,226 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: 00:10:37 13917613 reads; of these: 13917613 (100.00%) were paired; of these: 1173587 (8.43%) aligned concordantly 0 times 11588271 (83.26%) aligned concordantly exactly 1 time 1155755 (8.30%) aligned concordantly >1 times ---- 1173587 pairs aligned concordantly 0 times; of these: 279867 (23.85%) aligned discordantly 1 time ---- 893720 pairs aligned 0 times concordantly or discordantly; of these: 1787440 mates make up the pairs; of these: 1508241 (84.38%) aligned 0 times 174317 (9.75%) aligned exactly 1 time 104882 (5.87%) aligned >1 times 94.58% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 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 8 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] 779926 / 12997302 = 0.0600 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:59:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.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 @ Tue, 10 Dec 2019 14:59:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:59:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:59:12: 1000000 INFO @ Tue, 10 Dec 2019 14:59:19: 2000000 INFO @ Tue, 10 Dec 2019 14:59:27: 3000000 INFO @ Tue, 10 Dec 2019 14:59:34: 4000000 INFO @ Tue, 10 Dec 2019 14:59:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.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 @ Tue, 10 Dec 2019 14:59:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:59:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:59:42: 5000000 INFO @ Tue, 10 Dec 2019 14:59:42: 1000000 INFO @ Tue, 10 Dec 2019 14:59:49: 6000000 INFO @ Tue, 10 Dec 2019 14:59:50: 2000000 INFO @ Tue, 10 Dec 2019 14:59:57: 7000000 INFO @ Tue, 10 Dec 2019 14:59:58: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 15:00:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.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 @ Tue, 10 Dec 2019 15:00:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:00:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:00:04: 8000000 INFO @ Tue, 10 Dec 2019 15:00:06: 4000000 INFO @ Tue, 10 Dec 2019 15:00:12: 1000000 INFO @ Tue, 10 Dec 2019 15:00:12: 9000000 INFO @ Tue, 10 Dec 2019 15:00:13: 5000000 INFO @ Tue, 10 Dec 2019 15:00:19: 2000000 INFO @ Tue, 10 Dec 2019 15:00:20: 10000000 INFO @ Tue, 10 Dec 2019 15:00:21: 6000000 INFO @ Tue, 10 Dec 2019 15:00:27: 3000000 INFO @ Tue, 10 Dec 2019 15:00:27: 11000000 INFO @ Tue, 10 Dec 2019 15:00:29: 7000000 INFO @ Tue, 10 Dec 2019 15:00:34: 4000000 INFO @ Tue, 10 Dec 2019 15:00:34: 12000000 INFO @ Tue, 10 Dec 2019 15:00:36: 8000000 INFO @ Tue, 10 Dec 2019 15:00:41: 5000000 INFO @ Tue, 10 Dec 2019 15:00:42: 13000000 INFO @ Tue, 10 Dec 2019 15:00:44: 9000000 INFO @ Tue, 10 Dec 2019 15:00:50: 6000000 INFO @ Tue, 10 Dec 2019 15:00:50: 14000000 INFO @ Tue, 10 Dec 2019 15:00:52: 10000000 INFO @ Tue, 10 Dec 2019 15:00:57: 7000000 INFO @ Tue, 10 Dec 2019 15:00:58: 15000000 INFO @ Tue, 10 Dec 2019 15:01:00: 11000000 INFO @ Tue, 10 Dec 2019 15:01:04: 8000000 INFO @ Tue, 10 Dec 2019 15:01:07: 16000000 INFO @ Tue, 10 Dec 2019 15:01:08: 12000000 INFO @ Tue, 10 Dec 2019 15:01:12: 9000000 INFO @ Tue, 10 Dec 2019 15:01:15: 17000000 INFO @ Tue, 10 Dec 2019 15:01:16: 13000000 INFO @ Tue, 10 Dec 2019 15:01:19: 10000000 INFO @ Tue, 10 Dec 2019 15:01:24: 14000000 INFO @ Tue, 10 Dec 2019 15:01:24: 18000000 INFO @ Tue, 10 Dec 2019 15:01:26: 11000000 INFO @ Tue, 10 Dec 2019 15:01:31: 15000000 INFO @ Tue, 10 Dec 2019 15:01:32: 19000000 INFO @ Tue, 10 Dec 2019 15:01:33: 12000000 INFO @ Tue, 10 Dec 2019 15:01:40: 16000000 INFO @ Tue, 10 Dec 2019 15:01:40: 13000000 INFO @ Tue, 10 Dec 2019 15:01:40: 20000000 INFO @ Tue, 10 Dec 2019 15:01:48: 14000000 INFO @ Tue, 10 Dec 2019 15:01:48: 21000000 INFO @ Tue, 10 Dec 2019 15:01:49: 17000000 INFO @ Tue, 10 Dec 2019 15:01:55: 15000000 INFO @ Tue, 10 Dec 2019 15:01:56: 22000000 INFO @ Tue, 10 Dec 2019 15:01:57: 18000000 INFO @ Tue, 10 Dec 2019 15:02:02: 16000000 INFO @ Tue, 10 Dec 2019 15:02:05: 23000000 INFO @ Tue, 10 Dec 2019 15:02:05: 19000000 INFO @ Tue, 10 Dec 2019 15:02:10: 17000000 INFO @ Tue, 10 Dec 2019 15:02:13: 24000000 INFO @ Tue, 10 Dec 2019 15:02:14: 20000000 INFO @ Tue, 10 Dec 2019 15:02:17: 18000000 INFO @ Tue, 10 Dec 2019 15:02:19: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:02:19: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:02:19: #1 total tags in treatment: 11976365 INFO @ Tue, 10 Dec 2019 15:02:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:02:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 15:02:20: #1 tags after filtering in treatment: 7554340 INFO @ Tue, 10 Dec 2019 15:02:20: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 10 Dec 2019 15:02:20: #1 finished! INFO @ Tue, 10 Dec 2019 15:02:20: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:02:20: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:02:20: 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 @ Tue, 10 Dec 2019 15:02:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.05_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/sacCer3/SRX6742724/SRX6742724.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:02:21: 21000000 INFO @ Tue, 10 Dec 2019 15:02:24: 19000000 INFO @ Tue, 10 Dec 2019 15:02:29: 22000000 INFO @ Tue, 10 Dec 2019 15:02:32: 20000000 INFO @ Tue, 10 Dec 2019 15:02:36: 23000000 INFO @ Tue, 10 Dec 2019 15:02:39: 21000000 INFO @ Tue, 10 Dec 2019 15:02:43: 24000000 INFO @ Tue, 10 Dec 2019 15:02:46: 22000000 INFO @ Tue, 10 Dec 2019 15:02:48: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:02:48: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:02:48: #1 total tags in treatment: 11976365 INFO @ Tue, 10 Dec 2019 15:02:48: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:02:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 15:02:49: #1 tags after filtering in treatment: 7554340 INFO @ Tue, 10 Dec 2019 15:02:49: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 10 Dec 2019 15:02:49: #1 finished! INFO @ Tue, 10 Dec 2019 15:02:49: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:02:49: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:02:49: 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 @ Tue, 10 Dec 2019 15:02:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.10_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/SRX6742724/SRX6742724.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:02:53: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 15:03:00: 24000000 INFO @ Tue, 10 Dec 2019 15:03:05: #1 tag size is determined as 42 bps INFO @ Tue, 10 Dec 2019 15:03:05: #1 tag size = 42 INFO @ Tue, 10 Dec 2019 15:03:05: #1 total tags in treatment: 11976365 INFO @ Tue, 10 Dec 2019 15:03:05: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:03:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 15:03:06: #1 tags after filtering in treatment: 7554340 INFO @ Tue, 10 Dec 2019 15:03:06: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 10 Dec 2019 15:03:06: #1 finished! INFO @ Tue, 10 Dec 2019 15:03:06: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:03:06: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:03:06: 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 @ Tue, 10 Dec 2019 15:03:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.20_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/SRX6742724/SRX6742724.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6742724/SRX6742724.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。