Job ID = 2589973 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,788,149 reads read : 30,788,149 reads written : 30,788,149 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: 00:05:57 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171812 (0.56%) aligned 0 times 25273606 (82.09%) aligned exactly 1 time 5342731 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4710993 / 30616337 = 0.1539 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 @ Mon, 12 Aug 2019 19:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:16:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:16:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:17:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:17:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:17:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:17:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:17:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:17:06: 1000000 INFO @ Mon, 12 Aug 2019 19:17:08: 1000000 INFO @ Mon, 12 Aug 2019 19:17:09: 1000000 INFO @ Mon, 12 Aug 2019 19:17:14: 2000000 INFO @ Mon, 12 Aug 2019 19:17:16: 2000000 INFO @ Mon, 12 Aug 2019 19:17:16: 2000000 INFO @ Mon, 12 Aug 2019 19:17:21: 3000000 INFO @ Mon, 12 Aug 2019 19:17:23: 3000000 INFO @ Mon, 12 Aug 2019 19:17:25: 3000000 INFO @ Mon, 12 Aug 2019 19:17:28: 4000000 INFO @ Mon, 12 Aug 2019 19:17:30: 4000000 INFO @ Mon, 12 Aug 2019 19:17:33: 4000000 INFO @ Mon, 12 Aug 2019 19:17:35: 5000000 INFO @ Mon, 12 Aug 2019 19:17:38: 5000000 INFO @ Mon, 12 Aug 2019 19:17:41: 5000000 INFO @ Mon, 12 Aug 2019 19:17:42: 6000000 INFO @ Mon, 12 Aug 2019 19:17:45: 6000000 INFO @ Mon, 12 Aug 2019 19:17:49: 7000000 INFO @ Mon, 12 Aug 2019 19:17:50: 6000000 INFO @ Mon, 12 Aug 2019 19:17:52: 7000000 INFO @ Mon, 12 Aug 2019 19:17:57: 8000000 INFO @ Mon, 12 Aug 2019 19:17:58: 7000000 INFO @ Mon, 12 Aug 2019 19:17:59: 8000000 INFO @ Mon, 12 Aug 2019 19:18:04: 9000000 INFO @ Mon, 12 Aug 2019 19:18:06: 9000000 INFO @ Mon, 12 Aug 2019 19:18:06: 8000000 INFO @ Mon, 12 Aug 2019 19:18:11: 10000000 INFO @ Mon, 12 Aug 2019 19:18:13: 10000000 INFO @ Mon, 12 Aug 2019 19:18:15: 9000000 INFO @ Mon, 12 Aug 2019 19:18:18: 11000000 INFO @ Mon, 12 Aug 2019 19:18:21: 11000000 INFO @ Mon, 12 Aug 2019 19:18:23: 10000000 INFO @ Mon, 12 Aug 2019 19:18:25: 12000000 INFO @ Mon, 12 Aug 2019 19:18:28: 12000000 INFO @ Mon, 12 Aug 2019 19:18:31: 11000000 INFO @ Mon, 12 Aug 2019 19:18:32: 13000000 INFO @ Mon, 12 Aug 2019 19:18:35: 13000000 INFO @ Mon, 12 Aug 2019 19:18:40: 14000000 INFO @ Mon, 12 Aug 2019 19:18:40: 12000000 INFO @ Mon, 12 Aug 2019 19:18:42: 14000000 INFO @ Mon, 12 Aug 2019 19:18:47: 15000000 INFO @ Mon, 12 Aug 2019 19:18:48: 13000000 INFO @ Mon, 12 Aug 2019 19:18:49: 15000000 INFO @ Mon, 12 Aug 2019 19:18:54: 16000000 INFO @ Mon, 12 Aug 2019 19:18:56: 14000000 INFO @ Mon, 12 Aug 2019 19:18:56: 16000000 INFO @ Mon, 12 Aug 2019 19:19:01: 17000000 INFO @ Mon, 12 Aug 2019 19:19:04: 17000000 INFO @ Mon, 12 Aug 2019 19:19:05: 15000000 INFO @ Mon, 12 Aug 2019 19:19:08: 18000000 INFO @ Mon, 12 Aug 2019 19:19:11: 18000000 INFO @ Mon, 12 Aug 2019 19:19:13: 16000000 INFO @ Mon, 12 Aug 2019 19:19:15: 19000000 INFO @ Mon, 12 Aug 2019 19:19:18: 19000000 INFO @ Mon, 12 Aug 2019 19:19:21: 17000000 INFO @ Mon, 12 Aug 2019 19:19:22: 20000000 INFO @ Mon, 12 Aug 2019 19:19:25: 20000000 INFO @ Mon, 12 Aug 2019 19:19:29: 21000000 INFO @ Mon, 12 Aug 2019 19:19:30: 18000000 INFO @ Mon, 12 Aug 2019 19:19:32: 21000000 INFO @ Mon, 12 Aug 2019 19:19:37: 22000000 INFO @ Mon, 12 Aug 2019 19:19:38: 19000000 INFO @ Mon, 12 Aug 2019 19:19:39: 22000000 INFO @ Mon, 12 Aug 2019 19:19:44: 23000000 INFO @ Mon, 12 Aug 2019 19:19:47: 23000000 INFO @ Mon, 12 Aug 2019 19:19:47: 20000000 INFO @ Mon, 12 Aug 2019 19:19:51: 24000000 INFO @ Mon, 12 Aug 2019 19:19:54: 24000000 INFO @ Mon, 12 Aug 2019 19:19:55: 21000000 INFO @ Mon, 12 Aug 2019 19:19:58: 25000000 INFO @ Mon, 12 Aug 2019 19:20:01: 25000000 INFO @ Mon, 12 Aug 2019 19:20:04: 22000000 INFO @ Mon, 12 Aug 2019 19:20:05: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:20:05: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:20:05: #1 total tags in treatment: 25905344 INFO @ Mon, 12 Aug 2019 19:20:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:20:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:20:05: #1 tags after filtering in treatment: 25905344 INFO @ Mon, 12 Aug 2019 19:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:20:05: #1 finished! INFO @ Mon, 12 Aug 2019 19:20:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:20:08: #2 number of paired peaks: 131 WARNING @ Mon, 12 Aug 2019 19:20:08: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 12 Aug 2019 19:20:08: start model_add_line... INFO @ Mon, 12 Aug 2019 19:20:08: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:20:08: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:20:08: #1 total tags in treatment: 25905344 INFO @ Mon, 12 Aug 2019 19:20:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:20:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:20:08: start X-correlation... INFO @ Mon, 12 Aug 2019 19:20:08: end of X-cor INFO @ Mon, 12 Aug 2019 19:20:08: #2 finished! INFO @ Mon, 12 Aug 2019 19:20:08: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 19:20:08: #2 alternative fragment length(s) may be 0,31,167,293,311,389,445,534 bps INFO @ Mon, 12 Aug 2019 19:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.05_model.r WARNING @ Mon, 12 Aug 2019 19:20:08: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:20:08: #2 You may need to consider one of the other alternative d(s): 0,31,167,293,311,389,445,534 WARNING @ Mon, 12 Aug 2019 19:20:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:20:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:20:08: #1 tags after filtering in treatment: 25905344 INFO @ Mon, 12 Aug 2019 19:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:20:08: #1 finished! INFO @ Mon, 12 Aug 2019 19:20:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:20:10: #2 number of paired peaks: 131 WARNING @ Mon, 12 Aug 2019 19:20:10: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 12 Aug 2019 19:20:10: start model_add_line... INFO @ Mon, 12 Aug 2019 19:20:11: start X-correlation... INFO @ Mon, 12 Aug 2019 19:20:11: end of X-cor INFO @ Mon, 12 Aug 2019 19:20:11: #2 finished! INFO @ Mon, 12 Aug 2019 19:20:11: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 19:20:11: #2 alternative fragment length(s) may be 0,31,167,293,311,389,445,534 bps INFO @ Mon, 12 Aug 2019 19:20:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.20_model.r WARNING @ Mon, 12 Aug 2019 19:20:11: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:20:11: #2 You may need to consider one of the other alternative d(s): 0,31,167,293,311,389,445,534 WARNING @ Mon, 12 Aug 2019 19:20:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:20:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:20:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:20:12: 23000000 INFO @ Mon, 12 Aug 2019 19:20:20: 24000000 INFO @ Mon, 12 Aug 2019 19:20:28: 25000000 INFO @ Mon, 12 Aug 2019 19:20:36: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:20:36: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:20:36: #1 total tags in treatment: 25905344 INFO @ Mon, 12 Aug 2019 19:20:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:20:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:20:36: #1 tags after filtering in treatment: 25905344 INFO @ Mon, 12 Aug 2019 19:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:20:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:20:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:20:38: #2 number of paired peaks: 131 WARNING @ Mon, 12 Aug 2019 19:20:38: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 12 Aug 2019 19:20:38: start model_add_line... INFO @ Mon, 12 Aug 2019 19:20:39: start X-correlation... INFO @ Mon, 12 Aug 2019 19:20:39: end of X-cor INFO @ Mon, 12 Aug 2019 19:20:39: #2 finished! INFO @ Mon, 12 Aug 2019 19:20:39: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 19:20:39: #2 alternative fragment length(s) may be 0,31,167,293,311,389,445,534 bps INFO @ Mon, 12 Aug 2019 19:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466504/SRX466504.10_model.r WARNING @ Mon, 12 Aug 2019 19:20:39: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:20:39: #2 You may need to consider one of the other alternative d(s): 0,31,167,293,311,389,445,534 WARNING @ Mon, 12 Aug 2019 19:20:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:20:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:20:39: #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 SRX466504.05.bed: No such file or directory mv: cannot stat ‘SRX466504.05.bed’: No such file or directory /var/spool/uge/at091/job_scripts/2589973: line 335: 9073 Terminated MACS $i /var/spool/uge/at091/job_scripts/2589973: line 335: 9087 Terminated MACS $i /var/spool/uge/at091/job_scripts/2589973: line 335: 9101 Terminated MACS $i mv: cannot stat ‘SRX466504.05.bb’: No such file or directory ls: cannot access SRX466504.10.bed: No such file or directory mv: cannot stat ‘SRX466504.10.bed’: No such file or directory mv: cannot stat ‘SRX466504.10.bb’: No such file or directory ls: cannot access SRX466504.20.bed: No such file or directory mv: cannot stat ‘SRX466504.20.bed’: No such file or directory mv: cannot stat ‘SRX466504.20.bb’: No such file or directory