Job ID = 2010589 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:24:33 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 ) 2019-07-05T14:25:09 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 ) 2019-07-05T14:25:40 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 ) 2019-07-05T14:26:27 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 ) 2019-07-05T14:27:57 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 ) 2019-07-05T14:31:02 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 : 3,445,427 reads read : 6,890,854 reads written : 6,890,854 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: 00:01:15 3445427 reads; of these: 3445427 (100.00%) were paired; of these: 2340582 (67.93%) aligned concordantly 0 times 861422 (25.00%) aligned concordantly exactly 1 time 243423 (7.07%) aligned concordantly >1 times ---- 2340582 pairs aligned concordantly 0 times; of these: 41821 (1.79%) aligned discordantly 1 time ---- 2298761 pairs aligned 0 times concordantly or discordantly; of these: 4597522 mates make up the pairs; of these: 4526699 (98.46%) aligned 0 times 36288 (0.79%) aligned exactly 1 time 34535 (0.75%) aligned >1 times 34.31% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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_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] 37433 / 1145617 = 0.0327 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 @ Fri, 05 Jul 2019 23:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.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 @ Fri, 05 Jul 2019 23:34:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:34:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.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 @ Fri, 05 Jul 2019 23:34:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:34:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:34:32: 1000000 INFO @ Fri, 05 Jul 2019 23:34:32: 1000000 INFO @ Fri, 05 Jul 2019 23:34:39: 2000000 INFO @ Fri, 05 Jul 2019 23:34:39: 2000000 INFO @ Fri, 05 Jul 2019 23:34:41: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:34:41: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:34:41: #1 total tags in treatment: 1068190 INFO @ Fri, 05 Jul 2019 23:34:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:34:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:34:41: #1 tags after filtering in treatment: 859072 INFO @ Fri, 05 Jul 2019 23:34:41: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 23:34:41: #1 finished! INFO @ Fri, 05 Jul 2019 23:34:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:34:41: #2 number of paired peaks: 43 WARNING @ Fri, 05 Jul 2019 23:34:41: Too few paired peaks (43) 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 @ Fri, 05 Jul 2019 23:34:41: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:34:41: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:34:41: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:34:41: #1 total tags in treatment: 1068190 INFO @ Fri, 05 Jul 2019 23:34:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:34:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:34:41: #1 tags after filtering in treatment: 859072 INFO @ Fri, 05 Jul 2019 23:34:41: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 23:34:41: #1 finished! INFO @ Fri, 05 Jul 2019 23:34:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:34:41: #2 number of paired peaks: 43 WARNING @ Fri, 05 Jul 2019 23:34:41: Too few paired peaks (43) 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 @ Fri, 05 Jul 2019 23:34:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.05_model.r’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.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 @ Fri, 05 Jul 2019 23:35:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:35:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:35:16: 1000000 INFO @ Fri, 05 Jul 2019 23:35:23: 2000000 INFO @ Fri, 05 Jul 2019 23:35:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:35:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:35:25: #1 total tags in treatment: 1068190 INFO @ Fri, 05 Jul 2019 23:35:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:35:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:35:25: #1 tags after filtering in treatment: 859072 INFO @ Fri, 05 Jul 2019 23:35:25: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 23:35:25: #1 finished! INFO @ Fri, 05 Jul 2019 23:35:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:35:25: #2 number of paired peaks: 43 WARNING @ Fri, 05 Jul 2019 23:35:25: Too few paired peaks (43) 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 @ Fri, 05 Jul 2019 23:35:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.20_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/SRX381290/SRX381290.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381290/SRX381290.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。