Job ID = 4178477 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:30:05 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 : 31,035,337 reads read : 31,035,337 reads written : 31,035,337 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: 00:08:37 31035337 reads; of these: 31035337 (100.00%) were unpaired; of these: 549659 (1.77%) aligned 0 times 24371355 (78.53%) aligned exactly 1 time 6114323 (19.70%) aligned >1 times 98.23% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 14382787 / 30485678 = 0.4718 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:51:21: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:51:21: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:51:27: 1000000 INFO @ Thu, 05 Dec 2019 12:51:33: 2000000 INFO @ Thu, 05 Dec 2019 12:51:39: 3000000 INFO @ Thu, 05 Dec 2019 12:51:44: 4000000 INFO @ Thu, 05 Dec 2019 12:51:50: 5000000 INFO @ Thu, 05 Dec 2019 12:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:51:50: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:51:50: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:51:56: 1000000 INFO @ Thu, 05 Dec 2019 12:51:57: 6000000 INFO @ Thu, 05 Dec 2019 12:52:02: 2000000 INFO @ Thu, 05 Dec 2019 12:52:03: 7000000 INFO @ Thu, 05 Dec 2019 12:52:08: 3000000 INFO @ Thu, 05 Dec 2019 12:52:09: 8000000 INFO @ Thu, 05 Dec 2019 12:52:14: 4000000 INFO @ Thu, 05 Dec 2019 12:52:15: 9000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:52:20: 5000000 INFO @ Thu, 05 Dec 2019 12:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 12:52:20: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:52:20: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:52:21: 10000000 INFO @ Thu, 05 Dec 2019 12:52:26: 6000000 INFO @ Thu, 05 Dec 2019 12:52:27: 1000000 INFO @ Thu, 05 Dec 2019 12:52:28: 11000000 INFO @ Thu, 05 Dec 2019 12:52:32: 7000000 INFO @ Thu, 05 Dec 2019 12:52:33: 2000000 INFO @ Thu, 05 Dec 2019 12:52:34: 12000000 INFO @ Thu, 05 Dec 2019 12:52:38: 8000000 INFO @ Thu, 05 Dec 2019 12:52:40: 3000000 INFO @ Thu, 05 Dec 2019 12:52:40: 13000000 INFO @ Thu, 05 Dec 2019 12:52:44: 9000000 INFO @ Thu, 05 Dec 2019 12:52:46: 14000000 INFO @ Thu, 05 Dec 2019 12:52:46: 4000000 INFO @ Thu, 05 Dec 2019 12:52:50: 10000000 INFO @ Thu, 05 Dec 2019 12:52:53: 5000000 INFO @ Thu, 05 Dec 2019 12:52:53: 15000000 INFO @ Thu, 05 Dec 2019 12:52:56: 11000000 INFO @ Thu, 05 Dec 2019 12:52:59: 16000000 INFO @ Thu, 05 Dec 2019 12:52:59: 6000000 INFO @ Thu, 05 Dec 2019 12:53:00: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:53:00: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:53:00: #1 total tags in treatment: 16102891 INFO @ Thu, 05 Dec 2019 12:53:00: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:53:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:53:00: #1 tags after filtering in treatment: 16102891 INFO @ Thu, 05 Dec 2019 12:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:53:00: #1 finished! INFO @ Thu, 05 Dec 2019 12:53:00: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:53:01: #2 number of paired peaks: 576 WARNING @ Thu, 05 Dec 2019 12:53:01: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Thu, 05 Dec 2019 12:53:01: start model_add_line... INFO @ Thu, 05 Dec 2019 12:53:01: start X-correlation... INFO @ Thu, 05 Dec 2019 12:53:01: end of X-cor INFO @ Thu, 05 Dec 2019 12:53:01: #2 finished! INFO @ Thu, 05 Dec 2019 12:53:01: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 12:53:01: #2 alternative fragment length(s) may be 0,51,103,423,529 bps INFO @ Thu, 05 Dec 2019 12:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.05_model.r WARNING @ Thu, 05 Dec 2019 12:53:01: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:53:01: #2 You may need to consider one of the other alternative d(s): 0,51,103,423,529 WARNING @ Thu, 05 Dec 2019 12:53:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:53:01: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:53:01: 12000000 INFO @ Thu, 05 Dec 2019 12:53:05: 7000000 INFO @ Thu, 05 Dec 2019 12:53:07: 13000000 INFO @ Thu, 05 Dec 2019 12:53:12: 8000000 INFO @ Thu, 05 Dec 2019 12:53:12: 14000000 INFO @ Thu, 05 Dec 2019 12:53:18: 15000000 INFO @ Thu, 05 Dec 2019 12:53:18: 9000000 INFO @ Thu, 05 Dec 2019 12:53:23: 16000000 INFO @ Thu, 05 Dec 2019 12:53:24: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:53:24: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:53:24: #1 total tags in treatment: 16102891 INFO @ Thu, 05 Dec 2019 12:53:24: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:53:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:53:24: 10000000 INFO @ Thu, 05 Dec 2019 12:53:24: #1 tags after filtering in treatment: 16102891 INFO @ Thu, 05 Dec 2019 12:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:53:24: #1 finished! INFO @ Thu, 05 Dec 2019 12:53:24: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:53:25: #2 number of paired peaks: 576 WARNING @ Thu, 05 Dec 2019 12:53:25: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Thu, 05 Dec 2019 12:53:25: start model_add_line... INFO @ Thu, 05 Dec 2019 12:53:26: start X-correlation... INFO @ Thu, 05 Dec 2019 12:53:26: end of X-cor INFO @ Thu, 05 Dec 2019 12:53:26: #2 finished! INFO @ Thu, 05 Dec 2019 12:53:26: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 12:53:26: #2 alternative fragment length(s) may be 0,51,103,423,529 bps INFO @ Thu, 05 Dec 2019 12:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.10_model.r WARNING @ Thu, 05 Dec 2019 12:53:26: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:53:26: #2 You may need to consider one of the other alternative d(s): 0,51,103,423,529 WARNING @ Thu, 05 Dec 2019 12:53:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:53:26: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:53:31: 11000000 INFO @ Thu, 05 Dec 2019 12:53:37: 12000000 INFO @ Thu, 05 Dec 2019 12:53:44: 13000000 INFO @ Thu, 05 Dec 2019 12:53:51: 14000000 INFO @ Thu, 05 Dec 2019 12:53:57: 15000000 INFO @ Thu, 05 Dec 2019 12:54:04: 16000000 INFO @ Thu, 05 Dec 2019 12:54:05: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:54:05: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:54:05: #1 total tags in treatment: 16102891 INFO @ Thu, 05 Dec 2019 12:54:05: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:54:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:54:05: #1 tags after filtering in treatment: 16102891 INFO @ Thu, 05 Dec 2019 12:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:54:05: #1 finished! INFO @ Thu, 05 Dec 2019 12:54:05: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:54:06: #2 number of paired peaks: 576 WARNING @ Thu, 05 Dec 2019 12:54:06: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Thu, 05 Dec 2019 12:54:06: start model_add_line... INFO @ Thu, 05 Dec 2019 12:54:07: start X-correlation... INFO @ Thu, 05 Dec 2019 12:54:07: end of X-cor INFO @ Thu, 05 Dec 2019 12:54:07: #2 finished! INFO @ Thu, 05 Dec 2019 12:54:07: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 12:54:07: #2 alternative fragment length(s) may be 0,51,103,423,529 bps INFO @ Thu, 05 Dec 2019 12:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535380/SRX5535380.20_model.r WARNING @ Thu, 05 Dec 2019 12:54:07: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:54:07: #2 You may need to consider one of the other alternative d(s): 0,51,103,423,529 WARNING @ Thu, 05 Dec 2019 12:54:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:54:07: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:54:07: #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。 /var/spool/uge/it015/job_scripts/4178477: line 336: 8809 Terminated MACS $i /var/spool/uge/it015/job_scripts/4178477: line 336: 8890 Terminated MACS $i /var/spool/uge/it015/job_scripts/4178477: line 336: 9139 Terminated MACS $i ls: cannot access SRX5535380.05.bed: No such file or directory mv: cannot stat ‘SRX5535380.05.bed’: No such file or directory mv: cannot stat ‘SRX5535380.05.bb’: No such file or directory ls: cannot access SRX5535380.10.bed: No such file or directory mv: cannot stat ‘SRX5535380.10.bed’: No such file or directory mv: cannot stat ‘SRX5535380.10.bb’: No such file or directory ls: cannot access SRX5535380.20.bed: No such file or directory mv: cannot stat ‘SRX5535380.20.bed’: No such file or directory mv: cannot stat ‘SRX5535380.20.bb’: No such file or directory