Job ID = 6368081 SRX = SRX466544 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:53:03 prefetch.2.10.7: 1) Downloading 'SRR1163610'... 2020-06-15T23:53:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:57 prefetch.2.10.7: 1) 'SRR1163610' was downloaded successfully Read 30788149 spots for SRR1163610/SRR1163610.sra Written 30788149 spots for SRR1163610/SRR1163610.sra 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: 00:05:27 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169806 (0.55%) aligned 0 times 25275475 (82.09%) aligned exactly 1 time 5342868 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 4711366 / 30618343 = 0.1539 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 @ Tue, 16 Jun 2020 09:09:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:21: 1000000 INFO @ Tue, 16 Jun 2020 09:09:27: 2000000 INFO @ Tue, 16 Jun 2020 09:09:33: 3000000 INFO @ Tue, 16 Jun 2020 09:09:39: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 @ Tue, 16 Jun 2020 09:09:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:45: 5000000 INFO @ Tue, 16 Jun 2020 09:09:51: 1000000 INFO @ Tue, 16 Jun 2020 09:09:51: 6000000 INFO @ Tue, 16 Jun 2020 09:09:57: 2000000 INFO @ Tue, 16 Jun 2020 09:09:58: 7000000 INFO @ Tue, 16 Jun 2020 09:10:03: 3000000 INFO @ Tue, 16 Jun 2020 09:10:04: 8000000 INFO @ Tue, 16 Jun 2020 09:10:10: 4000000 INFO @ Tue, 16 Jun 2020 09:10:11: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 @ Tue, 16 Jun 2020 09:10:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:16: 5000000 INFO @ Tue, 16 Jun 2020 09:10:17: 10000000 INFO @ Tue, 16 Jun 2020 09:10:21: 1000000 INFO @ Tue, 16 Jun 2020 09:10:22: 6000000 INFO @ Tue, 16 Jun 2020 09:10:24: 11000000 INFO @ Tue, 16 Jun 2020 09:10:28: 2000000 INFO @ Tue, 16 Jun 2020 09:10:29: 7000000 INFO @ Tue, 16 Jun 2020 09:10:30: 12000000 INFO @ Tue, 16 Jun 2020 09:10:35: 3000000 INFO @ Tue, 16 Jun 2020 09:10:35: 8000000 INFO @ Tue, 16 Jun 2020 09:10:37: 13000000 INFO @ Tue, 16 Jun 2020 09:10:42: 4000000 INFO @ Tue, 16 Jun 2020 09:10:42: 9000000 INFO @ Tue, 16 Jun 2020 09:10:44: 14000000 INFO @ Tue, 16 Jun 2020 09:10:48: 10000000 INFO @ Tue, 16 Jun 2020 09:10:48: 5000000 INFO @ Tue, 16 Jun 2020 09:10:50: 15000000 INFO @ Tue, 16 Jun 2020 09:10:54: 11000000 INFO @ Tue, 16 Jun 2020 09:10:55: 6000000 INFO @ Tue, 16 Jun 2020 09:10:57: 16000000 INFO @ Tue, 16 Jun 2020 09:11:01: 12000000 INFO @ Tue, 16 Jun 2020 09:11:01: 7000000 INFO @ Tue, 16 Jun 2020 09:11:03: 17000000 INFO @ Tue, 16 Jun 2020 09:11:07: 13000000 INFO @ Tue, 16 Jun 2020 09:11:08: 8000000 INFO @ Tue, 16 Jun 2020 09:11:10: 18000000 INFO @ Tue, 16 Jun 2020 09:11:13: 14000000 INFO @ Tue, 16 Jun 2020 09:11:14: 9000000 INFO @ Tue, 16 Jun 2020 09:11:16: 19000000 INFO @ Tue, 16 Jun 2020 09:11:20: 15000000 INFO @ Tue, 16 Jun 2020 09:11:21: 10000000 INFO @ Tue, 16 Jun 2020 09:11:23: 20000000 INFO @ Tue, 16 Jun 2020 09:11:26: 16000000 INFO @ Tue, 16 Jun 2020 09:11:27: 11000000 INFO @ Tue, 16 Jun 2020 09:11:29: 21000000 INFO @ Tue, 16 Jun 2020 09:11:32: 17000000 INFO @ Tue, 16 Jun 2020 09:11:34: 12000000 INFO @ Tue, 16 Jun 2020 09:11:36: 22000000 INFO @ Tue, 16 Jun 2020 09:11:39: 18000000 INFO @ Tue, 16 Jun 2020 09:11:41: 13000000 INFO @ Tue, 16 Jun 2020 09:11:42: 23000000 INFO @ Tue, 16 Jun 2020 09:11:45: 19000000 INFO @ Tue, 16 Jun 2020 09:11:47: 14000000 INFO @ Tue, 16 Jun 2020 09:11:49: 24000000 INFO @ Tue, 16 Jun 2020 09:11:51: 20000000 INFO @ Tue, 16 Jun 2020 09:11:54: 15000000 INFO @ Tue, 16 Jun 2020 09:11:55: 25000000 INFO @ Tue, 16 Jun 2020 09:11:58: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:00: 16000000 INFO @ Tue, 16 Jun 2020 09:12:01: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:12:01: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:12:01: #1 total tags in treatment: 25906977 INFO @ Tue, 16 Jun 2020 09:12:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:02: #1 tags after filtering in treatment: 25906977 INFO @ Tue, 16 Jun 2020 09:12:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:03: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:12:03: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:04: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:12:04: #2 alternative fragment length(s) may be 0,27,382,401,416,418,452,535,571 bps INFO @ Tue, 16 Jun 2020 09:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:04: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:04: #2 You may need to consider one of the other alternative d(s): 0,27,382,401,416,418,452,535,571 WARNING @ Tue, 16 Jun 2020 09:12:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:12:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:04: 22000000 INFO @ Tue, 16 Jun 2020 09:12:07: 17000000 INFO @ Tue, 16 Jun 2020 09:12:10: 23000000 INFO @ Tue, 16 Jun 2020 09:12:13: 18000000 INFO @ Tue, 16 Jun 2020 09:12:17: 24000000 INFO @ Tue, 16 Jun 2020 09:12:19: 19000000 INFO @ Tue, 16 Jun 2020 09:12:24: 25000000 INFO @ Tue, 16 Jun 2020 09:12:25: 20000000 INFO @ Tue, 16 Jun 2020 09:12:30: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:12:30: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:12:30: #1 total tags in treatment: 25906977 INFO @ Tue, 16 Jun 2020 09:12:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:30: #1 tags after filtering in treatment: 25906977 INFO @ Tue, 16 Jun 2020 09:12:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:32: 21000000 INFO @ Tue, 16 Jun 2020 09:12:32: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:12:32: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:32: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2 alternative fragment length(s) may be 0,27,382,401,416,418,452,535,571 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466544/SRX466544.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:32: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:32: #2 You may need to consider one of the other alternative d(s): 0,27,382,401,416,418,452,535,571 WARNING @ Tue, 16 Jun 2020 09:12:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:12:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:38: 22000000 INFO @ Tue, 16 Jun 2020 09:12:44: 23000000 INFO @ Tue, 16 Jun 2020 09:12:50: 24000000 INFO @ Tue, 16 Jun 2020 09:12:56: 25000000 BigWig に変換しました。 /var/spool/uge/at143/job_scripts/6368081: line 271: 68711 Terminated MACS $i /var/spool/uge/at143/job_scripts/6368081: line 271: 79644 Terminated MACS $i /var/spool/uge/at143/job_scripts/6368081: line 271: 85022 Terminated MACS $i ls: cannot access SRX466544.05.bed: No such file or directory mv: cannot stat ‘SRX466544.05.bed’: No such file or directory 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