Job ID = 2010732 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:06:44 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 ) 2019-07-05T15:06:44 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 : 8,839,517 reads read : 17,679,034 reads written : 17,679,034 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: 00:00:00 Multiseed full-index search: 00:08:19 8839517 reads; of these: 8839517 (100.00%) were paired; of these: 1122680 (12.70%) aligned concordantly 0 times 6975591 (78.91%) aligned concordantly exactly 1 time 741246 (8.39%) aligned concordantly >1 times ---- 1122680 pairs aligned concordantly 0 times; of these: 117002 (10.42%) aligned discordantly 1 time ---- 1005678 pairs aligned 0 times concordantly or discordantly; of these: 2011356 mates make up the pairs; of these: 1733246 (86.17%) aligned 0 times 194780 (9.68%) aligned exactly 1 time 83330 (4.14%) aligned >1 times 90.20% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 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 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] 93062 / 7810334 = 0.0119 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 00:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.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, 06 Jul 2019 00:36:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:36:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.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, 06 Jul 2019 00:36:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:36:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.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, 06 Jul 2019 00:36:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:36:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:36:50: 1000000 INFO @ Sat, 06 Jul 2019 00:36:51: 1000000 INFO @ Sat, 06 Jul 2019 00:36:51: 1000000 INFO @ Sat, 06 Jul 2019 00:36:59: 2000000 INFO @ Sat, 06 Jul 2019 00:37:03: 2000000 INFO @ Sat, 06 Jul 2019 00:37:03: 2000000 INFO @ Sat, 06 Jul 2019 00:37:08: 3000000 INFO @ Sat, 06 Jul 2019 00:37:14: 3000000 INFO @ Sat, 06 Jul 2019 00:37:15: 3000000 INFO @ Sat, 06 Jul 2019 00:37:17: 4000000 INFO @ Sat, 06 Jul 2019 00:37:26: 4000000 INFO @ Sat, 06 Jul 2019 00:37:26: 5000000 INFO @ Sat, 06 Jul 2019 00:37:27: 4000000 INFO @ Sat, 06 Jul 2019 00:37:35: 6000000 INFO @ Sat, 06 Jul 2019 00:37:38: 5000000 INFO @ Sat, 06 Jul 2019 00:37:38: 5000000 INFO @ Sat, 06 Jul 2019 00:37:44: 7000000 INFO @ Sat, 06 Jul 2019 00:37:49: 6000000 INFO @ Sat, 06 Jul 2019 00:37:50: 6000000 INFO @ Sat, 06 Jul 2019 00:37:53: 8000000 INFO @ Sat, 06 Jul 2019 00:38:00: 7000000 INFO @ Sat, 06 Jul 2019 00:38:00: 7000000 INFO @ Sat, 06 Jul 2019 00:38:02: 9000000 INFO @ Sat, 06 Jul 2019 00:38:09: 8000000 INFO @ Sat, 06 Jul 2019 00:38:09: 8000000 INFO @ Sat, 06 Jul 2019 00:38:11: 10000000 INFO @ Sat, 06 Jul 2019 00:38:17: 9000000 INFO @ Sat, 06 Jul 2019 00:38:20: 9000000 INFO @ Sat, 06 Jul 2019 00:38:20: 11000000 INFO @ Sat, 06 Jul 2019 00:38:25: 10000000 INFO @ Sat, 06 Jul 2019 00:38:29: 12000000 INFO @ Sat, 06 Jul 2019 00:38:31: 10000000 INFO @ Sat, 06 Jul 2019 00:38:33: 11000000 INFO @ Sat, 06 Jul 2019 00:38:38: 13000000 INFO @ Sat, 06 Jul 2019 00:38:41: 12000000 INFO @ Sat, 06 Jul 2019 00:38:41: 11000000 INFO @ Sat, 06 Jul 2019 00:38:47: 14000000 INFO @ Sat, 06 Jul 2019 00:38:49: 13000000 INFO @ Sat, 06 Jul 2019 00:38:52: 12000000 INFO @ Sat, 06 Jul 2019 00:38:56: 15000000 INFO @ Sat, 06 Jul 2019 00:38:56: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:39:03: 13000000 INFO @ Sat, 06 Jul 2019 00:39:03: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:39:03: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:39:03: #1 total tags in treatment: 7624611 INFO @ Sat, 06 Jul 2019 00:39:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:39:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:39:03: #1 tags after filtering in treatment: 5951078 INFO @ Sat, 06 Jul 2019 00:39:03: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 06 Jul 2019 00:39:03: #1 finished! INFO @ Sat, 06 Jul 2019 00:39:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:39:03: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:39:03: 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, 06 Jul 2019 00:39:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.20_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/SRX386913/SRX386913.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:39:04: 15000000 INFO @ Sat, 06 Jul 2019 00:39:10: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:39:10: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:39:10: #1 total tags in treatment: 7624611 INFO @ Sat, 06 Jul 2019 00:39:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:39:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:39:11: #1 tags after filtering in treatment: 5951078 INFO @ Sat, 06 Jul 2019 00:39:11: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 06 Jul 2019 00:39:11: #1 finished! INFO @ Sat, 06 Jul 2019 00:39:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:39:11: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:39:11: 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, 06 Jul 2019 00:39:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.05_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/SRX386913/SRX386913.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:39:13: 14000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:39:23: 15000000 INFO @ Sat, 06 Jul 2019 00:39:31: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:39:31: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:39:31: #1 total tags in treatment: 7624611 INFO @ Sat, 06 Jul 2019 00:39:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:39:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:39:31: #1 tags after filtering in treatment: 5951078 INFO @ Sat, 06 Jul 2019 00:39:31: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 06 Jul 2019 00:39:31: #1 finished! INFO @ Sat, 06 Jul 2019 00:39:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:39:32: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:39:32: 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, 06 Jul 2019 00:39:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.10_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/SRX386913/SRX386913.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386913/SRX386913.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling