Job ID = 2640993 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:21:48 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 ) 2019-08-24T11:21:48 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 ) 2019-08-24T11:21:48 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 : 12,666,852 reads read : 25,333,704 reads written : 25,333,704 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: 00:16:19 12666852 reads; of these: 12666852 (100.00%) were paired; of these: 359464 (2.84%) aligned concordantly 0 times 10636748 (83.97%) aligned concordantly exactly 1 time 1670640 (13.19%) aligned concordantly >1 times ---- 359464 pairs aligned concordantly 0 times; of these: 86878 (24.17%) aligned discordantly 1 time ---- 272586 pairs aligned 0 times concordantly or discordantly; of these: 545172 mates make up the pairs; of these: 486579 (89.25%) aligned 0 times 25473 (4.67%) aligned exactly 1 time 33120 (6.08%) aligned >1 times 98.08% overall alignment rate Time searching: 00:16:19 Overall time: 00:16:19 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] 193803 / 12389743 = 0.0156 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:03:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.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 21:03:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:03:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:03:37: 1000000 INFO @ Sat, 24 Aug 2019 21:03:44: 2000000 INFO @ Sat, 24 Aug 2019 21:03:52: 3000000 INFO @ Sat, 24 Aug 2019 21:03:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.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 21:03:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:03:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:03:59: 4000000 INFO @ Sat, 24 Aug 2019 21:04:07: 5000000 INFO @ Sat, 24 Aug 2019 21:04:08: 1000000 INFO @ Sat, 24 Aug 2019 21:04:14: 6000000 INFO @ Sat, 24 Aug 2019 21:04:20: 2000000 INFO @ Sat, 24 Aug 2019 21:04:22: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.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 21:04:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:04:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:04:30: 8000000 INFO @ Sat, 24 Aug 2019 21:04:30: 3000000 INFO @ Sat, 24 Aug 2019 21:04:38: 9000000 INFO @ Sat, 24 Aug 2019 21:04:38: 1000000 INFO @ Sat, 24 Aug 2019 21:04:41: 4000000 INFO @ Sat, 24 Aug 2019 21:04:45: 10000000 INFO @ Sat, 24 Aug 2019 21:04:46: 2000000 INFO @ Sat, 24 Aug 2019 21:04:52: 5000000 INFO @ Sat, 24 Aug 2019 21:04:53: 11000000 INFO @ Sat, 24 Aug 2019 21:04:55: 3000000 INFO @ Sat, 24 Aug 2019 21:05:01: 12000000 INFO @ Sat, 24 Aug 2019 21:05:02: 6000000 INFO @ Sat, 24 Aug 2019 21:05:04: 4000000 INFO @ Sat, 24 Aug 2019 21:05:09: 13000000 INFO @ Sat, 24 Aug 2019 21:05:13: 7000000 INFO @ Sat, 24 Aug 2019 21:05:13: 5000000 INFO @ Sat, 24 Aug 2019 21:05:16: 14000000 INFO @ Sat, 24 Aug 2019 21:05:21: 6000000 INFO @ Sat, 24 Aug 2019 21:05:23: 8000000 INFO @ Sat, 24 Aug 2019 21:05:24: 15000000 INFO @ Sat, 24 Aug 2019 21:05:30: 7000000 INFO @ Sat, 24 Aug 2019 21:05:32: 16000000 INFO @ Sat, 24 Aug 2019 21:05:33: 9000000 INFO @ Sat, 24 Aug 2019 21:05:39: 8000000 INFO @ Sat, 24 Aug 2019 21:05:42: 17000000 INFO @ Sat, 24 Aug 2019 21:05:44: 10000000 INFO @ Sat, 24 Aug 2019 21:05:47: 9000000 INFO @ Sat, 24 Aug 2019 21:05:51: 18000000 INFO @ Sat, 24 Aug 2019 21:05:54: 11000000 INFO @ Sat, 24 Aug 2019 21:05:56: 10000000 INFO @ Sat, 24 Aug 2019 21:05:59: 19000000 INFO @ Sat, 24 Aug 2019 21:06:05: 12000000 INFO @ Sat, 24 Aug 2019 21:06:05: 11000000 INFO @ Sat, 24 Aug 2019 21:06:06: 20000000 INFO @ Sat, 24 Aug 2019 21:06:13: 12000000 INFO @ Sat, 24 Aug 2019 21:06:14: 21000000 INFO @ Sat, 24 Aug 2019 21:06:15: 13000000 INFO @ Sat, 24 Aug 2019 21:06:22: 22000000 INFO @ Sat, 24 Aug 2019 21:06:22: 13000000 INFO @ Sat, 24 Aug 2019 21:06:25: 14000000 INFO @ Sat, 24 Aug 2019 21:06:30: 23000000 INFO @ Sat, 24 Aug 2019 21:06:31: 14000000 INFO @ Sat, 24 Aug 2019 21:06:36: 15000000 INFO @ Sat, 24 Aug 2019 21:06:37: 24000000 INFO @ Sat, 24 Aug 2019 21:06:39: 15000000 INFO @ Sat, 24 Aug 2019 21:06:41: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:06:41: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:06:41: #1 total tags in treatment: 12114104 INFO @ Sat, 24 Aug 2019 21:06:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:06:41: #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 21:06:41: #1 tags after filtering in treatment: 8811671 INFO @ Sat, 24 Aug 2019 21:06:41: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:06:41: #1 finished! INFO @ Sat, 24 Aug 2019 21:06:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:06:42: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:06:42: 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 21:06:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.05_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/SRX4936099/SRX4936099.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:06:45: 16000000 INFO @ Sat, 24 Aug 2019 21:06:48: 16000000 INFO @ Sat, 24 Aug 2019 21:06:53: 17000000 INFO @ Sat, 24 Aug 2019 21:06:59: 17000000 INFO @ Sat, 24 Aug 2019 21:07:03: 18000000 INFO @ Sat, 24 Aug 2019 21:07:08: 18000000 INFO @ Sat, 24 Aug 2019 21:07:13: 19000000 INFO @ Sat, 24 Aug 2019 21:07:16: 19000000 INFO @ Sat, 24 Aug 2019 21:07:24: 20000000 INFO @ Sat, 24 Aug 2019 21:07:25: 20000000 INFO @ Sat, 24 Aug 2019 21:07:34: 21000000 INFO @ Sat, 24 Aug 2019 21:07:35: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:07:43: 22000000 INFO @ Sat, 24 Aug 2019 21:07:45: 22000000 INFO @ Sat, 24 Aug 2019 21:07:51: 23000000 INFO @ Sat, 24 Aug 2019 21:07:56: 23000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:08:00: 24000000 INFO @ Sat, 24 Aug 2019 21:08:04: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:08:04: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:08:04: #1 total tags in treatment: 12114104 INFO @ Sat, 24 Aug 2019 21:08:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:08:04: #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 21:08:04: #1 tags after filtering in treatment: 8811671 INFO @ Sat, 24 Aug 2019 21:08:04: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:08:04: #1 finished! INFO @ Sat, 24 Aug 2019 21:08:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:08:05: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:08:05: 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 21:08:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.20_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/SRX4936099/SRX4936099.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:08:06: 24000000 INFO @ Sat, 24 Aug 2019 21:08:11: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:08:11: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:08:11: #1 total tags in treatment: 12114104 INFO @ Sat, 24 Aug 2019 21:08:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:08:11: #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 21:08:11: #1 tags after filtering in treatment: 8811671 INFO @ Sat, 24 Aug 2019 21:08:11: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:08:11: #1 finished! INFO @ Sat, 24 Aug 2019 21:08:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:08:12: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:08:12: 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 21:08:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.10_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/SRX4936099/SRX4936099.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936099/SRX4936099.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling