Job ID = 2007994 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:01:15 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 ) 2019-07-05T08:01:15 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 : 1,898,333 reads read : 3,796,666 reads written : 3,796,666 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: 00:04:37 1898333 reads; of these: 1898333 (100.00%) were paired; of these: 199620 (10.52%) aligned concordantly 0 times 1564706 (82.43%) aligned concordantly exactly 1 time 134007 (7.06%) aligned concordantly >1 times ---- 199620 pairs aligned concordantly 0 times; of these: 110725 (55.47%) aligned discordantly 1 time ---- 88895 pairs aligned 0 times concordantly or discordantly; of these: 177790 mates make up the pairs; of these: 130910 (73.63%) aligned 0 times 23059 (12.97%) aligned exactly 1 time 23821 (13.40%) aligned >1 times 96.55% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 6593 / 1807281 = 0.0036 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 17:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.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 17:10:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:10:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.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 17:10:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:10:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.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 17:10:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:10:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:10:30: 1000000 INFO @ Fri, 05 Jul 2019 17:10:36: 1000000 INFO @ Fri, 05 Jul 2019 17:10:36: 1000000 INFO @ Fri, 05 Jul 2019 17:10:40: 2000000 INFO @ Fri, 05 Jul 2019 17:10:47: 2000000 INFO @ Fri, 05 Jul 2019 17:10:49: 3000000 INFO @ Fri, 05 Jul 2019 17:10:49: 2000000 INFO @ Fri, 05 Jul 2019 17:10:55: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:10:55: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:10:55: #1 total tags in treatment: 1692381 INFO @ Fri, 05 Jul 2019 17:10:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:10:55: #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 17:10:55: #1 tags after filtering in treatment: 1588678 INFO @ Fri, 05 Jul 2019 17:10:55: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:10:55: #1 finished! INFO @ Fri, 05 Jul 2019 17:10:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:10:55: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 17:10:55: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 17:10:55: start model_add_line... INFO @ Fri, 05 Jul 2019 17:10:55: start X-correlation... INFO @ Fri, 05 Jul 2019 17:10:55: end of X-cor INFO @ Fri, 05 Jul 2019 17:10:55: #2 finished! INFO @ Fri, 05 Jul 2019 17:10:55: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 17:10:55: #2 alternative fragment length(s) may be 0,22,49,70,109,130,147,175,203,248,261,293,311,328,351,372,391,431,458,479,498,521,542,560,582,596,598 bps INFO @ Fri, 05 Jul 2019 17:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.05_model.r WARNING @ Fri, 05 Jul 2019 17:10:55: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:10:55: #2 You may need to consider one of the other alternative d(s): 0,22,49,70,109,130,147,175,203,248,261,293,311,328,351,372,391,431,458,479,498,521,542,560,582,596,598 WARNING @ Fri, 05 Jul 2019 17:10:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:10:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:10:59: 3000000 INFO @ Fri, 05 Jul 2019 17:11:02: 3000000 INFO @ Fri, 05 Jul 2019 17:11:06: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:11:06: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:11:06: #1 total tags in treatment: 1692381 INFO @ Fri, 05 Jul 2019 17:11:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:11:06: #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 17:11:06: #1 tags after filtering in treatment: 1588678 INFO @ Fri, 05 Jul 2019 17:11:06: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:11:06: #1 finished! INFO @ Fri, 05 Jul 2019 17:11:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:11:07: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 17:11:07: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 17:11:07: start model_add_line... INFO @ Fri, 05 Jul 2019 17:11:07: start X-correlation... INFO @ Fri, 05 Jul 2019 17:11:07: end of X-cor INFO @ Fri, 05 Jul 2019 17:11:07: #2 finished! INFO @ Fri, 05 Jul 2019 17:11:07: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 17:11:07: #2 alternative fragment length(s) may be 0,22,49,70,109,130,147,175,203,248,261,293,311,328,351,372,391,431,458,479,498,521,542,560,582,596,598 bps INFO @ Fri, 05 Jul 2019 17:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.20_model.r WARNING @ Fri, 05 Jul 2019 17:11:07: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:11:07: #2 You may need to consider one of the other alternative d(s): 0,22,49,70,109,130,147,175,203,248,261,293,311,328,351,372,391,431,458,479,498,521,542,560,582,596,598 WARNING @ Fri, 05 Jul 2019 17:11:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:11:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:11:11: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:11:11: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:11:11: #1 total tags in treatment: 1692381 INFO @ Fri, 05 Jul 2019 17:11:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:11:11: #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 17:11:11: #1 tags after filtering in treatment: 1588678 INFO @ Fri, 05 Jul 2019 17:11:11: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:11:11: #1 finished! INFO @ Fri, 05 Jul 2019 17:11:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:11:11: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 17:11:11: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 17:11:11: start model_add_line... INFO @ Fri, 05 Jul 2019 17:11:11: start X-correlation... INFO @ Fri, 05 Jul 2019 17:11:11: end of X-cor INFO @ Fri, 05 Jul 2019 17:11:11: #2 finished! INFO @ Fri, 05 Jul 2019 17:11:11: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 17:11:11: #2 alternative fragment length(s) may be 0,22,49,70,109,130,147,175,203,248,261,293,311,328,351,372,391,431,458,479,498,521,542,560,582,596,598 bps INFO @ Fri, 05 Jul 2019 17:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471784/ERX471784.10_model.r WARNING @ Fri, 05 Jul 2019 17:11:11: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:11:11: #2 You may need to consider one of the other alternative d(s): 0,22,49,70,109,130,147,175,203,248,261,293,311,328,351,372,391,431,458,479,498,521,542,560,582,596,598 WARNING @ Fri, 05 Jul 2019 17:11:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:11:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:11:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 ls: cannot access ERX471784.05.bed: No such file or directory mv: cannot stat ‘ERX471784.05.bed’: No such file or directory /var/spool/uge/at123/job_scripts/2007994: line 335: 31786 Terminated MACS $i /var/spool/uge/at123/job_scripts/2007994: line 335: 31801 Terminated MACS $i /var/spool/uge/at123/job_scripts/2007994: line 335: 31814 Terminated MACS $i mv: cannot stat ‘ERX471784.05.bb’: No such file or directory ls: cannot access ERX471784.10.bed: No such file or directory mv: cannot stat ‘ERX471784.10.bed’: No such file or directory mv: cannot stat ‘ERX471784.10.bb’: No such file or directory ls: cannot access ERX471784.20.bed: No such file or directory mv: cannot stat ‘ERX471784.20.bed’: No such file or directory mv: cannot stat ‘ERX471784.20.bb’: No such file or directory