Job ID = 2641002 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:17:07 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 ) 2019-08-24T11:17:07 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 ) 2019-08-24T11:17:07 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 ) 2019-08-24T11:34:11 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 ) 2019-08-24T11:34:11 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 : 16,567,266 reads read : 33,134,532 reads written : 33,134,532 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: 00:21:22 16567266 reads; of these: 16567266 (100.00%) were paired; of these: 2355398 (14.22%) aligned concordantly 0 times 12202370 (73.65%) aligned concordantly exactly 1 time 2009498 (12.13%) aligned concordantly >1 times ---- 2355398 pairs aligned concordantly 0 times; of these: 1275292 (54.14%) aligned discordantly 1 time ---- 1080106 pairs aligned 0 times concordantly or discordantly; of these: 2160212 mates make up the pairs; of these: 1487634 (68.87%) aligned 0 times 222386 (10.29%) aligned exactly 1 time 450192 (20.84%) aligned >1 times 95.51% overall alignment rate Time searching: 00:21:22 Overall time: 00:21:22 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 16 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] 1115432 / 15484586 = 0.0720 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.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 21:23:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:23:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:23:27: 1000000 INFO @ Sat, 24 Aug 2019 21:23:35: 2000000 INFO @ Sat, 24 Aug 2019 21:23:43: 3000000 INFO @ Sat, 24 Aug 2019 21:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.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 21:23:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:23:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:23:51: 4000000 INFO @ Sat, 24 Aug 2019 21:23:58: 1000000 INFO @ Sat, 24 Aug 2019 21:24:00: 5000000 INFO @ Sat, 24 Aug 2019 21:24:07: 2000000 INFO @ Sat, 24 Aug 2019 21:24:08: 6000000 INFO @ Sat, 24 Aug 2019 21:24:16: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:24:17: 7000000 INFO @ Sat, 24 Aug 2019 21:24:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.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 21:24:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:24:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:24:25: 8000000 INFO @ Sat, 24 Aug 2019 21:24:25: 4000000 INFO @ Sat, 24 Aug 2019 21:24:29: 1000000 INFO @ Sat, 24 Aug 2019 21:24:33: 9000000 INFO @ Sat, 24 Aug 2019 21:24:34: 5000000 INFO @ Sat, 24 Aug 2019 21:24:39: 2000000 INFO @ Sat, 24 Aug 2019 21:24:42: 10000000 INFO @ Sat, 24 Aug 2019 21:24:44: 6000000 INFO @ Sat, 24 Aug 2019 21:24:50: 3000000 INFO @ Sat, 24 Aug 2019 21:24:50: 11000000 INFO @ Sat, 24 Aug 2019 21:24:53: 7000000 INFO @ Sat, 24 Aug 2019 21:24:58: 12000000 INFO @ Sat, 24 Aug 2019 21:25:00: 4000000 INFO @ Sat, 24 Aug 2019 21:25:02: 8000000 INFO @ Sat, 24 Aug 2019 21:25:07: 13000000 INFO @ Sat, 24 Aug 2019 21:25:10: 5000000 INFO @ Sat, 24 Aug 2019 21:25:11: 9000000 INFO @ Sat, 24 Aug 2019 21:25:15: 14000000 INFO @ Sat, 24 Aug 2019 21:25:20: 10000000 INFO @ Sat, 24 Aug 2019 21:25:21: 6000000 INFO @ Sat, 24 Aug 2019 21:25:23: 15000000 INFO @ Sat, 24 Aug 2019 21:25:30: 11000000 INFO @ Sat, 24 Aug 2019 21:25:32: 7000000 INFO @ Sat, 24 Aug 2019 21:25:32: 16000000 INFO @ Sat, 24 Aug 2019 21:25:39: 12000000 INFO @ Sat, 24 Aug 2019 21:25:40: 17000000 INFO @ Sat, 24 Aug 2019 21:25:42: 8000000 INFO @ Sat, 24 Aug 2019 21:25:48: 13000000 INFO @ Sat, 24 Aug 2019 21:25:48: 18000000 INFO @ Sat, 24 Aug 2019 21:25:52: 9000000 INFO @ Sat, 24 Aug 2019 21:25:57: 19000000 INFO @ Sat, 24 Aug 2019 21:25:57: 14000000 INFO @ Sat, 24 Aug 2019 21:26:03: 10000000 INFO @ Sat, 24 Aug 2019 21:26:05: 20000000 INFO @ Sat, 24 Aug 2019 21:26:06: 15000000 INFO @ Sat, 24 Aug 2019 21:26:13: 11000000 INFO @ Sat, 24 Aug 2019 21:26:13: 21000000 INFO @ Sat, 24 Aug 2019 21:26:15: 16000000 INFO @ Sat, 24 Aug 2019 21:26:22: 22000000 INFO @ Sat, 24 Aug 2019 21:26:24: 12000000 INFO @ Sat, 24 Aug 2019 21:26:25: 17000000 INFO @ Sat, 24 Aug 2019 21:26:30: 23000000 INFO @ Sat, 24 Aug 2019 21:26:34: 18000000 INFO @ Sat, 24 Aug 2019 21:26:34: 13000000 INFO @ Sat, 24 Aug 2019 21:26:39: 24000000 INFO @ Sat, 24 Aug 2019 21:26:43: 19000000 INFO @ Sat, 24 Aug 2019 21:26:45: 14000000 INFO @ Sat, 24 Aug 2019 21:26:47: 25000000 INFO @ Sat, 24 Aug 2019 21:26:52: 20000000 INFO @ Sat, 24 Aug 2019 21:26:55: 26000000 INFO @ Sat, 24 Aug 2019 21:26:55: 15000000 INFO @ Sat, 24 Aug 2019 21:27:01: 21000000 INFO @ Sat, 24 Aug 2019 21:27:04: 27000000 INFO @ Sat, 24 Aug 2019 21:27:06: 16000000 INFO @ Sat, 24 Aug 2019 21:27:10: 22000000 INFO @ Sat, 24 Aug 2019 21:27:12: 28000000 INFO @ Sat, 24 Aug 2019 21:27:16: 17000000 INFO @ Sat, 24 Aug 2019 21:27:19: 23000000 INFO @ Sat, 24 Aug 2019 21:27:20: 29000000 INFO @ Sat, 24 Aug 2019 21:27:24: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:27:24: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:27:24: #1 total tags in treatment: 13142714 INFO @ Sat, 24 Aug 2019 21:27:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:27:24: #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 21:27:24: #1 tags after filtering in treatment: 9143540 INFO @ Sat, 24 Aug 2019 21:27:24: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 24 Aug 2019 21:27:24: #1 finished! INFO @ Sat, 24 Aug 2019 21:27:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:27:25: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:27:25: 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 21:27:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.05_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/SRX4936108/SRX4936108.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:27:27: 18000000 INFO @ Sat, 24 Aug 2019 21:27:28: 24000000 INFO @ Sat, 24 Aug 2019 21:27:38: 25000000 INFO @ Sat, 24 Aug 2019 21:27:38: 19000000 INFO @ Sat, 24 Aug 2019 21:27:47: 26000000 INFO @ Sat, 24 Aug 2019 21:27:48: 20000000 INFO @ Sat, 24 Aug 2019 21:27:56: 27000000 INFO @ Sat, 24 Aug 2019 21:27:59: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:28:05: 28000000 INFO @ Sat, 24 Aug 2019 21:28:09: 22000000 INFO @ Sat, 24 Aug 2019 21:28:14: 29000000 INFO @ Sat, 24 Aug 2019 21:28:18: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:28:18: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:28:18: #1 total tags in treatment: 13142714 INFO @ Sat, 24 Aug 2019 21:28:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:28:18: #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 21:28:18: #1 tags after filtering in treatment: 9143540 INFO @ Sat, 24 Aug 2019 21:28:18: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 24 Aug 2019 21:28:18: #1 finished! INFO @ Sat, 24 Aug 2019 21:28:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:28:18: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:28:19: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:28:19: 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 21:28:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.10_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/SRX4936108/SRX4936108.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:28:19: 23000000 INFO @ Sat, 24 Aug 2019 21:28:30: 24000000 INFO @ Sat, 24 Aug 2019 21:28:40: 25000000 INFO @ Sat, 24 Aug 2019 21:28:50: 26000000 INFO @ Sat, 24 Aug 2019 21:29:00: 27000000 INFO @ Sat, 24 Aug 2019 21:29:10: 28000000 INFO @ Sat, 24 Aug 2019 21:29:20: 29000000 INFO @ Sat, 24 Aug 2019 21:29:24: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:29:24: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:29:24: #1 total tags in treatment: 13142714 INFO @ Sat, 24 Aug 2019 21:29:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:29:24: #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 21:29:25: #1 tags after filtering in treatment: 9143540 INFO @ Sat, 24 Aug 2019 21:29:25: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 24 Aug 2019 21:29:25: #1 finished! INFO @ Sat, 24 Aug 2019 21:29:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:29:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:29:25: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:29:25: 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 21:29:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.20_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/SRX4936108/SRX4936108.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936108/SRX4936108.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling