Job ID = 2590082 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,570,721 reads read : 32,570,721 reads written : 32,570,721 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: 00:08:55 32570721 reads; of these: 32570721 (100.00%) were unpaired; of these: 779437 (2.39%) aligned 0 times 25992191 (79.80%) aligned exactly 1 time 5799093 (17.80%) aligned >1 times 97.61% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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 16 files... [bam_rmdupse_core] 5125329 / 31791284 = 0.1612 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 20:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.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 20:00:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.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 20:00:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.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 20:00:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:56: 1000000 INFO @ Mon, 12 Aug 2019 20:00:57: 1000000 INFO @ Mon, 12 Aug 2019 20:00:57: 1000000 INFO @ Mon, 12 Aug 2019 20:01:03: 2000000 INFO @ Mon, 12 Aug 2019 20:01:04: 2000000 INFO @ Mon, 12 Aug 2019 20:01:04: 2000000 INFO @ Mon, 12 Aug 2019 20:01:09: 3000000 INFO @ Mon, 12 Aug 2019 20:01:10: 3000000 INFO @ Mon, 12 Aug 2019 20:01:10: 3000000 INFO @ Mon, 12 Aug 2019 20:01:16: 4000000 INFO @ Mon, 12 Aug 2019 20:01:16: 4000000 INFO @ Mon, 12 Aug 2019 20:01:17: 4000000 INFO @ Mon, 12 Aug 2019 20:01:23: 5000000 INFO @ Mon, 12 Aug 2019 20:01:23: 5000000 INFO @ Mon, 12 Aug 2019 20:01:24: 5000000 INFO @ Mon, 12 Aug 2019 20:01:29: 6000000 INFO @ Mon, 12 Aug 2019 20:01:31: 6000000 INFO @ Mon, 12 Aug 2019 20:01:31: 6000000 INFO @ Mon, 12 Aug 2019 20:01:36: 7000000 INFO @ Mon, 12 Aug 2019 20:01:39: 7000000 INFO @ Mon, 12 Aug 2019 20:01:39: 7000000 INFO @ Mon, 12 Aug 2019 20:01:43: 8000000 INFO @ Mon, 12 Aug 2019 20:01:46: 8000000 INFO @ Mon, 12 Aug 2019 20:01:47: 8000000 INFO @ Mon, 12 Aug 2019 20:01:50: 9000000 INFO @ Mon, 12 Aug 2019 20:01:53: 9000000 INFO @ Mon, 12 Aug 2019 20:01:55: 9000000 INFO @ Mon, 12 Aug 2019 20:01:56: 10000000 INFO @ Mon, 12 Aug 2019 20:02:00: 10000000 INFO @ Mon, 12 Aug 2019 20:02:02: 10000000 INFO @ Mon, 12 Aug 2019 20:02:03: 11000000 INFO @ Mon, 12 Aug 2019 20:02:08: 11000000 INFO @ Mon, 12 Aug 2019 20:02:10: 12000000 INFO @ Mon, 12 Aug 2019 20:02:10: 11000000 INFO @ Mon, 12 Aug 2019 20:02:15: 12000000 INFO @ Mon, 12 Aug 2019 20:02:16: 13000000 INFO @ Mon, 12 Aug 2019 20:02:18: 12000000 INFO @ Mon, 12 Aug 2019 20:02:22: 13000000 INFO @ Mon, 12 Aug 2019 20:02:23: 14000000 INFO @ Mon, 12 Aug 2019 20:02:25: 13000000 INFO @ Mon, 12 Aug 2019 20:02:29: 14000000 INFO @ Mon, 12 Aug 2019 20:02:30: 15000000 INFO @ Mon, 12 Aug 2019 20:02:33: 14000000 INFO @ Mon, 12 Aug 2019 20:02:36: 16000000 INFO @ Mon, 12 Aug 2019 20:02:37: 15000000 INFO @ Mon, 12 Aug 2019 20:02:40: 15000000 INFO @ Mon, 12 Aug 2019 20:02:43: 17000000 INFO @ Mon, 12 Aug 2019 20:02:44: 16000000 INFO @ Mon, 12 Aug 2019 20:02:48: 16000000 INFO @ Mon, 12 Aug 2019 20:02:50: 18000000 INFO @ Mon, 12 Aug 2019 20:02:51: 17000000 INFO @ Mon, 12 Aug 2019 20:02:56: 17000000 INFO @ Mon, 12 Aug 2019 20:02:56: 19000000 INFO @ Mon, 12 Aug 2019 20:02:58: 18000000 INFO @ Mon, 12 Aug 2019 20:03:03: 18000000 INFO @ Mon, 12 Aug 2019 20:03:03: 20000000 INFO @ Mon, 12 Aug 2019 20:03:05: 19000000 INFO @ Mon, 12 Aug 2019 20:03:10: 21000000 INFO @ Mon, 12 Aug 2019 20:03:10: 19000000 INFO @ Mon, 12 Aug 2019 20:03:12: 20000000 INFO @ Mon, 12 Aug 2019 20:03:16: 20000000 INFO @ Mon, 12 Aug 2019 20:03:16: 22000000 INFO @ Mon, 12 Aug 2019 20:03:19: 21000000 INFO @ Mon, 12 Aug 2019 20:03:23: 21000000 INFO @ Mon, 12 Aug 2019 20:03:23: 23000000 INFO @ Mon, 12 Aug 2019 20:03:26: 22000000 INFO @ Mon, 12 Aug 2019 20:03:29: 22000000 INFO @ Mon, 12 Aug 2019 20:03:30: 24000000 INFO @ Mon, 12 Aug 2019 20:03:34: 23000000 INFO @ Mon, 12 Aug 2019 20:03:36: 23000000 INFO @ Mon, 12 Aug 2019 20:03:36: 25000000 INFO @ Mon, 12 Aug 2019 20:03:41: 24000000 INFO @ Mon, 12 Aug 2019 20:03:43: 26000000 INFO @ Mon, 12 Aug 2019 20:03:43: 24000000 INFO @ Mon, 12 Aug 2019 20:03:48: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:03:48: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:03:48: #1 total tags in treatment: 26665955 INFO @ Mon, 12 Aug 2019 20:03:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:03:48: #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 20:03:48: 25000000 INFO @ Mon, 12 Aug 2019 20:03:48: #1 tags after filtering in treatment: 26665955 INFO @ Mon, 12 Aug 2019 20:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:03:48: #1 finished! INFO @ Mon, 12 Aug 2019 20:03:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:03:50: #2 number of paired peaks: 125 WARNING @ Mon, 12 Aug 2019 20:03:50: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 12 Aug 2019 20:03:50: start model_add_line... INFO @ Mon, 12 Aug 2019 20:03:51: start X-correlation... INFO @ Mon, 12 Aug 2019 20:03:51: end of X-cor INFO @ Mon, 12 Aug 2019 20:03:51: #2 finished! INFO @ Mon, 12 Aug 2019 20:03:51: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:03:51: #2 alternative fragment length(s) may be 0,46,185,449,521,575 bps INFO @ Mon, 12 Aug 2019 20:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.05_model.r WARNING @ Mon, 12 Aug 2019 20:03:51: #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 20:03:51: #2 You may need to consider one of the other alternative d(s): 0,46,185,449,521,575 WARNING @ Mon, 12 Aug 2019 20:03:51: #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 20:03:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:03:51: 25000000 INFO @ Mon, 12 Aug 2019 20:03:55: 26000000 INFO @ Mon, 12 Aug 2019 20:03:58: 26000000 INFO @ Mon, 12 Aug 2019 20:04:00: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:04:00: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:04:00: #1 total tags in treatment: 26665955 INFO @ Mon, 12 Aug 2019 20:04:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:04:00: #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 20:04:00: #1 tags after filtering in treatment: 26665955 INFO @ Mon, 12 Aug 2019 20:04:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:04:00: #1 finished! INFO @ Mon, 12 Aug 2019 20:04:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:04:03: #2 number of paired peaks: 125 WARNING @ Mon, 12 Aug 2019 20:04:03: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 12 Aug 2019 20:04:03: start model_add_line... INFO @ Mon, 12 Aug 2019 20:04:03: start X-correlation... INFO @ Mon, 12 Aug 2019 20:04:03: end of X-cor INFO @ Mon, 12 Aug 2019 20:04:03: #2 finished! INFO @ Mon, 12 Aug 2019 20:04:03: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:04:03: #2 alternative fragment length(s) may be 0,46,185,449,521,575 bps INFO @ Mon, 12 Aug 2019 20:04:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.10_model.r WARNING @ Mon, 12 Aug 2019 20:04:03: #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 20:04:03: #2 You may need to consider one of the other alternative d(s): 0,46,185,449,521,575 WARNING @ Mon, 12 Aug 2019 20:04:03: #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 20:04:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:04:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:04:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:04:03: #1 total tags in treatment: 26665955 INFO @ Mon, 12 Aug 2019 20:04:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:04:03: #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 20:04:04: #1 tags after filtering in treatment: 26665955 INFO @ Mon, 12 Aug 2019 20:04:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:04:04: #1 finished! INFO @ Mon, 12 Aug 2019 20:04:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:04:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:04:06: #2 number of paired peaks: 125 WARNING @ Mon, 12 Aug 2019 20:04:06: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 12 Aug 2019 20:04:06: start model_add_line... INFO @ Mon, 12 Aug 2019 20:04:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:04:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:04:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:04:06: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:04:06: #2 alternative fragment length(s) may be 0,46,185,449,521,575 bps INFO @ Mon, 12 Aug 2019 20:04:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494924/SRX494924.20_model.r WARNING @ Mon, 12 Aug 2019 20:04:06: #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 20:04:06: #2 You may need to consider one of the other alternative d(s): 0,46,185,449,521,575 WARNING @ Mon, 12 Aug 2019 20:04:06: #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 20:04:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:04:06: #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 SRX494924.05.bed: No such file or directory mv: cannot stat ‘SRX494924.05.bed’: No such file or directory /var/spool/uge/at121/job_scripts/2590082: line 335: 10322 Terminated MACS $i /var/spool/uge/at121/job_scripts/2590082: line 335: 10336 Terminated MACS $i /var/spool/uge/at121/job_scripts/2590082: line 335: 10350 Terminated MACS $i mv: cannot stat ‘SRX494924.05.bb’: No such file or directory ls: cannot access SRX494924.10.bed: No such file or directory mv: cannot stat ‘SRX494924.10.bed’: No such file or directory mv: cannot stat ‘SRX494924.10.bb’: No such file or directory ls: cannot access SRX494924.20.bed: No such file or directory mv: cannot stat ‘SRX494924.20.bed’: No such file or directory mv: cannot stat ‘SRX494924.20.bb’: No such file or directory