Job ID = 6366302 SRX = SRX1078726 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:44 prefetch.2.10.7: 1) Downloading 'SRR2084333'... 2020-06-15T23:44:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:17 prefetch.2.10.7: 1) 'SRR2084333' was downloaded successfully Read 29066908 spots for SRR2084333/SRR2084333.sra Written 29066908 spots for SRR2084333/SRR2084333.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: 00:00:01 Multiseed full-index search: 00:07:34 29066908 reads; of these: 29066908 (100.00%) were unpaired; of these: 401620 (1.38%) aligned 0 times 23673932 (81.45%) aligned exactly 1 time 4991356 (17.17%) aligned >1 times 98.62% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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 12 files... [bam_rmdupse_core] 4065781 / 28665288 = 0.1418 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 09:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.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 09:08:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:06: 1000000 INFO @ Tue, 16 Jun 2020 09:09:14: 2000000 INFO @ Tue, 16 Jun 2020 09:09:22: 3000000 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 09:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.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 09:09:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:29: 4000000 INFO @ Tue, 16 Jun 2020 09:09:36: 1000000 INFO @ Tue, 16 Jun 2020 09:09:37: 5000000 INFO @ Tue, 16 Jun 2020 09:09:45: 2000000 INFO @ Tue, 16 Jun 2020 09:09:46: 6000000 INFO @ Tue, 16 Jun 2020 09:09:53: 3000000 INFO @ Tue, 16 Jun 2020 09:09:54: 7000000 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 09:09:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.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 09:09:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:01: 4000000 INFO @ Tue, 16 Jun 2020 09:10:02: 8000000 INFO @ Tue, 16 Jun 2020 09:10:06: 1000000 INFO @ Tue, 16 Jun 2020 09:10:09: 5000000 INFO @ Tue, 16 Jun 2020 09:10:11: 9000000 INFO @ Tue, 16 Jun 2020 09:10:15: 2000000 INFO @ Tue, 16 Jun 2020 09:10:18: 6000000 INFO @ Tue, 16 Jun 2020 09:10:19: 10000000 INFO @ Tue, 16 Jun 2020 09:10:24: 3000000 INFO @ Tue, 16 Jun 2020 09:10:27: 7000000 INFO @ Tue, 16 Jun 2020 09:10:28: 11000000 INFO @ Tue, 16 Jun 2020 09:10:32: 4000000 INFO @ Tue, 16 Jun 2020 09:10:36: 8000000 INFO @ Tue, 16 Jun 2020 09:10:37: 12000000 INFO @ Tue, 16 Jun 2020 09:10:40: 5000000 INFO @ Tue, 16 Jun 2020 09:10:44: 9000000 INFO @ Tue, 16 Jun 2020 09:10:45: 13000000 INFO @ Tue, 16 Jun 2020 09:10:48: 6000000 INFO @ Tue, 16 Jun 2020 09:10:53: 10000000 INFO @ Tue, 16 Jun 2020 09:10:54: 14000000 INFO @ Tue, 16 Jun 2020 09:10:57: 7000000 INFO @ Tue, 16 Jun 2020 09:11:01: 11000000 INFO @ Tue, 16 Jun 2020 09:11:03: 15000000 INFO @ Tue, 16 Jun 2020 09:11:05: 8000000 INFO @ Tue, 16 Jun 2020 09:11:10: 12000000 INFO @ Tue, 16 Jun 2020 09:11:11: 16000000 INFO @ Tue, 16 Jun 2020 09:11:14: 9000000 INFO @ Tue, 16 Jun 2020 09:11:19: 13000000 INFO @ Tue, 16 Jun 2020 09:11:20: 17000000 INFO @ Tue, 16 Jun 2020 09:11:22: 10000000 INFO @ Tue, 16 Jun 2020 09:11:27: 14000000 INFO @ Tue, 16 Jun 2020 09:11:29: 18000000 INFO @ Tue, 16 Jun 2020 09:11:31: 11000000 INFO @ Tue, 16 Jun 2020 09:11:36: 15000000 INFO @ Tue, 16 Jun 2020 09:11:37: 19000000 INFO @ Tue, 16 Jun 2020 09:11:39: 12000000 INFO @ Tue, 16 Jun 2020 09:11:44: 16000000 INFO @ Tue, 16 Jun 2020 09:11:45: 20000000 INFO @ Tue, 16 Jun 2020 09:11:48: 13000000 INFO @ Tue, 16 Jun 2020 09:11:52: 17000000 INFO @ Tue, 16 Jun 2020 09:11:53: 21000000 INFO @ Tue, 16 Jun 2020 09:11:56: 14000000 INFO @ Tue, 16 Jun 2020 09:12:00: 18000000 INFO @ Tue, 16 Jun 2020 09:12:01: 22000000 INFO @ Tue, 16 Jun 2020 09:12:04: 15000000 INFO @ Tue, 16 Jun 2020 09:12:08: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:10: 23000000 INFO @ Tue, 16 Jun 2020 09:12:13: 16000000 INFO @ Tue, 16 Jun 2020 09:12:16: 20000000 INFO @ Tue, 16 Jun 2020 09:12:18: 24000000 INFO @ Tue, 16 Jun 2020 09:12:21: 17000000 INFO @ Tue, 16 Jun 2020 09:12:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:23: #1 total tags in treatment: 24599507 INFO @ Tue, 16 Jun 2020 09:12:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:23: #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 09:12:24: #1 tags after filtering in treatment: 24599507 INFO @ Tue, 16 Jun 2020 09:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:25: 21000000 INFO @ Tue, 16 Jun 2020 09:12:25: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 09:12:25: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:26: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:12:26: #2 alternative fragment length(s) may be 0,20,39,584 bps INFO @ Tue, 16 Jun 2020 09:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:26: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:26: #2 You may need to consider one of the other alternative d(s): 0,20,39,584 WARNING @ Tue, 16 Jun 2020 09:12:26: #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 09:12:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:29: 18000000 INFO @ Tue, 16 Jun 2020 09:12:32: 22000000 INFO @ Tue, 16 Jun 2020 09:12:37: 19000000 INFO @ Tue, 16 Jun 2020 09:12:39: 23000000 INFO @ Tue, 16 Jun 2020 09:12:45: 20000000 INFO @ Tue, 16 Jun 2020 09:12:46: 24000000 INFO @ Tue, 16 Jun 2020 09:12:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:51: #1 total tags in treatment: 24599507 INFO @ Tue, 16 Jun 2020 09:12:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:51: #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 09:12:51: #1 tags after filtering in treatment: 24599507 INFO @ Tue, 16 Jun 2020 09:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:53: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 09:12:53: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:53: 21000000 INFO @ Tue, 16 Jun 2020 09:12:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:53: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:12:53: #2 alternative fragment length(s) may be 0,20,39,584 bps INFO @ Tue, 16 Jun 2020 09:12:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078726/SRX1078726.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:53: #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 09:12:53: #2 You may need to consider one of the other alternative d(s): 0,20,39,584 WARNING @ Tue, 16 Jun 2020 09:12:53: #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 09:12:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:00: 22000000 INFO @ Tue, 16 Jun 2020 09:13:08: 23000000 INFO @ Tue, 16 Jun 2020 09:13:16: 24000000 BigWig に変換しました。 /var/spool/uge/it024/job_scripts/6366302: line 271: 17613 Terminated MACS $i /var/spool/uge/it024/job_scripts/6366302: line 271: 32440 Terminated MACS $i /var/spool/uge/it024/job_scripts/6366302: line 271: 14930 Terminated MACS $i ls: cannot access SRX1078726.05.bed: No such file or directory mv: cannot stat ‘SRX1078726.05.bed’: No such file or directory mv: cannot stat ‘SRX1078726.05.bb’: No such file or directory ls: cannot access SRX1078726.10.bed: No such file or directory mv: cannot stat ‘SRX1078726.10.bed’: No such file or directory mv: cannot stat ‘SRX1078726.10.bb’: No such file or directory ls: cannot access SRX1078726.20.bed: No such file or directory mv: cannot stat ‘SRX1078726.20.bed’: No such file or directory mv: cannot stat ‘SRX1078726.20.bb’: No such file or directory