Job ID = 2010708 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:12:20 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 ) spots read : 11,235,769 reads read : 22,471,538 reads written : 22,471,538 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: 00:10:36 11235769 reads; of these: 11235769 (100.00%) were paired; of these: 1617791 (14.40%) aligned concordantly 0 times 8806301 (78.38%) aligned concordantly exactly 1 time 811677 (7.22%) aligned concordantly >1 times ---- 1617791 pairs aligned concordantly 0 times; of these: 140609 (8.69%) aligned discordantly 1 time ---- 1477182 pairs aligned 0 times concordantly or discordantly; of these: 2954364 mates make up the pairs; of these: 2626794 (88.91%) aligned 0 times 235380 (7.97%) aligned exactly 1 time 92190 (3.12%) aligned >1 times 88.31% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 125096 / 9729811 = 0.0129 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 00:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.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 00:38:49: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:38:49: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.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 00:38:50: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:38:50: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:38:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.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 00:38:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:38:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:39:00: 1000000 INFO @ Sat, 06 Jul 2019 00:39:01: 1000000 INFO @ Sat, 06 Jul 2019 00:39:01: 1000000 INFO @ Sat, 06 Jul 2019 00:39:09: 2000000 INFO @ Sat, 06 Jul 2019 00:39:10: 2000000 INFO @ Sat, 06 Jul 2019 00:39:11: 2000000 INFO @ Sat, 06 Jul 2019 00:39:17: 3000000 INFO @ Sat, 06 Jul 2019 00:39:20: 3000000 INFO @ Sat, 06 Jul 2019 00:39:21: 3000000 INFO @ Sat, 06 Jul 2019 00:39:24: 4000000 INFO @ Sat, 06 Jul 2019 00:39:29: 4000000 INFO @ Sat, 06 Jul 2019 00:39:31: 4000000 INFO @ Sat, 06 Jul 2019 00:39:32: 5000000 INFO @ Sat, 06 Jul 2019 00:39:39: 5000000 INFO @ Sat, 06 Jul 2019 00:39:39: 6000000 INFO @ Sat, 06 Jul 2019 00:39:41: 5000000 INFO @ Sat, 06 Jul 2019 00:39:47: 7000000 INFO @ Sat, 06 Jul 2019 00:39:49: 6000000 INFO @ Sat, 06 Jul 2019 00:39:50: 6000000 INFO @ Sat, 06 Jul 2019 00:39:54: 8000000 INFO @ Sat, 06 Jul 2019 00:39:59: 7000000 INFO @ Sat, 06 Jul 2019 00:40:00: 7000000 INFO @ Sat, 06 Jul 2019 00:40:02: 9000000 INFO @ Sat, 06 Jul 2019 00:40:09: 8000000 INFO @ Sat, 06 Jul 2019 00:40:09: 8000000 INFO @ Sat, 06 Jul 2019 00:40:10: 10000000 INFO @ Sat, 06 Jul 2019 00:40:17: 11000000 INFO @ Sat, 06 Jul 2019 00:40:19: 9000000 INFO @ Sat, 06 Jul 2019 00:40:19: 9000000 INFO @ Sat, 06 Jul 2019 00:40:25: 12000000 INFO @ Sat, 06 Jul 2019 00:40:29: 10000000 INFO @ Sat, 06 Jul 2019 00:40:30: 10000000 INFO @ Sat, 06 Jul 2019 00:40:32: 13000000 INFO @ Sat, 06 Jul 2019 00:40:39: 11000000 INFO @ Sat, 06 Jul 2019 00:40:40: 14000000 INFO @ Sat, 06 Jul 2019 00:40:40: 11000000 INFO @ Sat, 06 Jul 2019 00:40:47: 15000000 INFO @ Sat, 06 Jul 2019 00:40:48: 12000000 INFO @ Sat, 06 Jul 2019 00:40:50: 12000000 INFO @ Sat, 06 Jul 2019 00:40:55: 16000000 INFO @ Sat, 06 Jul 2019 00:40:58: 13000000 INFO @ Sat, 06 Jul 2019 00:41:00: 13000000 INFO @ Sat, 06 Jul 2019 00:41:02: 17000000 INFO @ Sat, 06 Jul 2019 00:41:08: 14000000 INFO @ Sat, 06 Jul 2019 00:41:10: 18000000 INFO @ Sat, 06 Jul 2019 00:41:10: 14000000 INFO @ Sat, 06 Jul 2019 00:41:17: 19000000 INFO @ Sat, 06 Jul 2019 00:41:18: 15000000 INFO @ Sat, 06 Jul 2019 00:41:20: 15000000 INFO @ Sat, 06 Jul 2019 00:41:22: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:41:22: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:41:22: #1 total tags in treatment: 9493810 INFO @ Sat, 06 Jul 2019 00:41:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:41:22: #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 00:41:22: #1 tags after filtering in treatment: 6977979 INFO @ Sat, 06 Jul 2019 00:41:22: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:41:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:41:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:41:23: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:41:23: 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 00:41:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.20_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/SRX386889/SRX386889.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:41:27: 16000000 INFO @ Sat, 06 Jul 2019 00:41:30: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:41:37: 17000000 INFO @ Sat, 06 Jul 2019 00:41:40: 17000000 INFO @ Sat, 06 Jul 2019 00:41:47: 18000000 INFO @ Sat, 06 Jul 2019 00:41:49: 18000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:41:56: 19000000 INFO @ Sat, 06 Jul 2019 00:41:59: 19000000 INFO @ Sat, 06 Jul 2019 00:42:02: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:42:02: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:42:02: #1 total tags in treatment: 9493810 INFO @ Sat, 06 Jul 2019 00:42:02: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:42:02: #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 00:42:02: #1 tags after filtering in treatment: 6977979 INFO @ Sat, 06 Jul 2019 00:42:02: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:42:02: #1 finished! INFO @ Sat, 06 Jul 2019 00:42:02: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:42:03: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:42:03: 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 00:42:03: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:42:05: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:42:05: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:42:05: #1 total tags in treatment: 9493810 INFO @ Sat, 06 Jul 2019 00:42:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:42:05: #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 00:42:05: #1 tags after filtering in treatment: 6977979 INFO @ Sat, 06 Jul 2019 00:42:05: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:42:05: #1 finished! INFO @ Sat, 06 Jul 2019 00:42:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:42:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:42:06: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:42:06: 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 @ Sat, 06 Jul 2019 00:42:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.10_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/SRX386889/SRX386889.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386889/SRX386889.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling