Job ID = 1292530 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:16:00 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T10:16:00 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra36/SRR/001136/SRR1163610' 2019-06-02T10:16:00 fasterq-dump.2.9.6 err: invalid accession 'SRR1163610' 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 rm: cannot remove ‘fastqDump_tmp*’: 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: 00:09:34 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171798 (0.56%) aligned 0 times 25273719 (82.09%) aligned exactly 1 time 5342632 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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] 4711001 / 30616351 = 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 @ Sun, 02 Jun 2019 19:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.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 @ Sun, 02 Jun 2019 19:49:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:49:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.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 @ Sun, 02 Jun 2019 19:49:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:49:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.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 @ Sun, 02 Jun 2019 19:49:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:49:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:49:31: 1000000 INFO @ Sun, 02 Jun 2019 19:49:31: 1000000 INFO @ Sun, 02 Jun 2019 19:49:31: 1000000 INFO @ Sun, 02 Jun 2019 19:49:43: 2000000 INFO @ Sun, 02 Jun 2019 19:49:43: 2000000 INFO @ Sun, 02 Jun 2019 19:49:44: 2000000 INFO @ Sun, 02 Jun 2019 19:49:56: 3000000 INFO @ Sun, 02 Jun 2019 19:49:56: 3000000 INFO @ Sun, 02 Jun 2019 19:49:57: 3000000 INFO @ Sun, 02 Jun 2019 19:50:08: 4000000 INFO @ Sun, 02 Jun 2019 19:50:08: 4000000 INFO @ Sun, 02 Jun 2019 19:50:09: 4000000 INFO @ Sun, 02 Jun 2019 19:50:19: 5000000 INFO @ Sun, 02 Jun 2019 19:50:21: 5000000 INFO @ Sun, 02 Jun 2019 19:50:22: 5000000 INFO @ Sun, 02 Jun 2019 19:50:31: 6000000 INFO @ Sun, 02 Jun 2019 19:50:34: 6000000 INFO @ Sun, 02 Jun 2019 19:50:35: 6000000 INFO @ Sun, 02 Jun 2019 19:50:42: 7000000 INFO @ Sun, 02 Jun 2019 19:50:47: 7000000 INFO @ Sun, 02 Jun 2019 19:50:47: 7000000 INFO @ Sun, 02 Jun 2019 19:50:53: 8000000 INFO @ Sun, 02 Jun 2019 19:50:59: 8000000 INFO @ Sun, 02 Jun 2019 19:50:59: 8000000 INFO @ Sun, 02 Jun 2019 19:51:05: 9000000 INFO @ Sun, 02 Jun 2019 19:51:11: 9000000 INFO @ Sun, 02 Jun 2019 19:51:12: 9000000 INFO @ Sun, 02 Jun 2019 19:51:16: 10000000 INFO @ Sun, 02 Jun 2019 19:51:24: 10000000 INFO @ Sun, 02 Jun 2019 19:51:24: 10000000 INFO @ Sun, 02 Jun 2019 19:51:28: 11000000 INFO @ Sun, 02 Jun 2019 19:51:37: 11000000 INFO @ Sun, 02 Jun 2019 19:51:37: 11000000 INFO @ Sun, 02 Jun 2019 19:51:40: 12000000 INFO @ Sun, 02 Jun 2019 19:51:48: 12000000 INFO @ Sun, 02 Jun 2019 19:51:49: 12000000 INFO @ Sun, 02 Jun 2019 19:51:51: 13000000 INFO @ Sun, 02 Jun 2019 19:51:59: 13000000 INFO @ Sun, 02 Jun 2019 19:52:01: 13000000 INFO @ Sun, 02 Jun 2019 19:52:03: 14000000 INFO @ Sun, 02 Jun 2019 19:52:10: 14000000 INFO @ Sun, 02 Jun 2019 19:52:13: 14000000 INFO @ Sun, 02 Jun 2019 19:52:14: 15000000 INFO @ Sun, 02 Jun 2019 19:52:22: 15000000 INFO @ Sun, 02 Jun 2019 19:52:25: 15000000 INFO @ Sun, 02 Jun 2019 19:52:25: 16000000 INFO @ Sun, 02 Jun 2019 19:52:33: 16000000 INFO @ Sun, 02 Jun 2019 19:52:37: 16000000 INFO @ Sun, 02 Jun 2019 19:52:37: 17000000 INFO @ Sun, 02 Jun 2019 19:52:44: 17000000 INFO @ Sun, 02 Jun 2019 19:52:48: 18000000 INFO @ Sun, 02 Jun 2019 19:52:49: 17000000 INFO @ Sun, 02 Jun 2019 19:52:56: 18000000 INFO @ Sun, 02 Jun 2019 19:52:59: 19000000 INFO @ Sun, 02 Jun 2019 19:53:01: 18000000 INFO @ Sun, 02 Jun 2019 19:53:07: 19000000 INFO @ Sun, 02 Jun 2019 19:53:11: 20000000 INFO @ Sun, 02 Jun 2019 19:53:14: 19000000 INFO @ Sun, 02 Jun 2019 19:53:18: 20000000 INFO @ Sun, 02 Jun 2019 19:53:23: 21000000 INFO @ Sun, 02 Jun 2019 19:53:25: 20000000 INFO @ Sun, 02 Jun 2019 19:53:29: 21000000 INFO @ Sun, 02 Jun 2019 19:53:34: 22000000 INFO @ Sun, 02 Jun 2019 19:53:37: 21000000 INFO @ Sun, 02 Jun 2019 19:53:41: 22000000 INFO @ Sun, 02 Jun 2019 19:53:45: 23000000 INFO @ Sun, 02 Jun 2019 19:53:50: 22000000 INFO @ Sun, 02 Jun 2019 19:53:52: 23000000 INFO @ Sun, 02 Jun 2019 19:53:57: 24000000 INFO @ Sun, 02 Jun 2019 19:54:02: 23000000 INFO @ Sun, 02 Jun 2019 19:54:03: 24000000 INFO @ Sun, 02 Jun 2019 19:54:08: 25000000 INFO @ Sun, 02 Jun 2019 19:54:14: 24000000 INFO @ Sun, 02 Jun 2019 19:54:14: 25000000 INFO @ Sun, 02 Jun 2019 19:54:18: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:54:18: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:54:18: #1 total tags in treatment: 25905350 INFO @ Sun, 02 Jun 2019 19:54:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:54:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:54:19: #1 tags after filtering in treatment: 25905350 INFO @ Sun, 02 Jun 2019 19:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:54:19: #1 finished! INFO @ Sun, 02 Jun 2019 19:54:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:54:22: #2 number of paired peaks: 144 WARNING @ Sun, 02 Jun 2019 19:54:22: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 02 Jun 2019 19:54:22: start model_add_line... INFO @ Sun, 02 Jun 2019 19:54:22: start X-correlation... INFO @ Sun, 02 Jun 2019 19:54:22: end of X-cor INFO @ Sun, 02 Jun 2019 19:54:22: #2 finished! INFO @ Sun, 02 Jun 2019 19:54:22: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:54:22: #2 alternative fragment length(s) may be 0,27,382,402,420,452,536,571 bps INFO @ Sun, 02 Jun 2019 19:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.20_model.r WARNING @ Sun, 02 Jun 2019 19:54:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:54:22: #2 You may need to consider one of the other alternative d(s): 0,27,382,402,420,452,536,571 WARNING @ Sun, 02 Jun 2019 19:54:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:54:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:54:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:54:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:54:25: #1 total tags in treatment: 25905350 INFO @ Sun, 02 Jun 2019 19:54:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:54:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:54:26: #1 tags after filtering in treatment: 25905350 INFO @ Sun, 02 Jun 2019 19:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:54:26: #1 finished! INFO @ Sun, 02 Jun 2019 19:54:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:54:27: 25000000 INFO @ Sun, 02 Jun 2019 19:54:29: #2 number of paired peaks: 144 WARNING @ Sun, 02 Jun 2019 19:54:29: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 02 Jun 2019 19:54:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:54:29: start X-correlation... INFO @ Sun, 02 Jun 2019 19:54:29: end of X-cor INFO @ Sun, 02 Jun 2019 19:54:29: #2 finished! INFO @ Sun, 02 Jun 2019 19:54:29: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:54:29: #2 alternative fragment length(s) may be 0,27,382,402,420,452,536,571 bps INFO @ Sun, 02 Jun 2019 19:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.05_model.r WARNING @ Sun, 02 Jun 2019 19:54:29: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:54:29: #2 You may need to consider one of the other alternative d(s): 0,27,382,402,420,452,536,571 WARNING @ Sun, 02 Jun 2019 19:54:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:54:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:54:38: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:54:38: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:54:38: #1 total tags in treatment: 25905350 INFO @ Sun, 02 Jun 2019 19:54:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:54:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:54:38: #1 tags after filtering in treatment: 25905350 INFO @ Sun, 02 Jun 2019 19:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:54:38: #1 finished! INFO @ Sun, 02 Jun 2019 19:54:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:54:41: #2 number of paired peaks: 144 WARNING @ Sun, 02 Jun 2019 19:54:41: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 02 Jun 2019 19:54:41: start model_add_line... INFO @ Sun, 02 Jun 2019 19:54:42: start X-correlation... INFO @ Sun, 02 Jun 2019 19:54:42: end of X-cor INFO @ Sun, 02 Jun 2019 19:54:42: #2 finished! INFO @ Sun, 02 Jun 2019 19:54:42: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:54:42: #2 alternative fragment length(s) may be 0,27,382,402,420,452,536,571 bps INFO @ Sun, 02 Jun 2019 19:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466544/SRX466544.10_model.r WARNING @ Sun, 02 Jun 2019 19:54:42: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:54:42: #2 You may need to consider one of the other alternative d(s): 0,27,382,402,420,452,536,571 WARNING @ Sun, 02 Jun 2019 19:54:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:54:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:54:42: #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 SRX466544.05.bed: No such file or directory mv: cannot stat ‘SRX466544.05.bed’: No such file or directory /var/spool/uge/at079/job_scripts/1292530: line 321: 49162 Terminated MACS $i /var/spool/uge/at079/job_scripts/1292530: line 321: 49163 Terminated MACS $i /var/spool/uge/at079/job_scripts/1292530: line 321: 49164 Terminated MACS $i mv: cannot stat ‘SRX466544.05.bb’: No such file or directory ls: cannot access SRX466544.10.bed: No such file or directory mv: cannot stat ‘SRX466544.10.bed’: No such file or directory mv: cannot stat ‘SRX466544.10.bb’: No such file or directory ls: cannot access SRX466544.20.bed: No such file or directory mv: cannot stat ‘SRX466544.20.bed’: No such file or directory mv: cannot stat ‘SRX466544.20.bb’: No such file or directory