Job ID = 6365849 SRX = SRX002676 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:31:15 prefetch.2.10.7: 1) Downloading 'SRR013613'... 2020-06-15T22:31:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:31:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:31:52 prefetch.2.10.7: 'SRR013613' is valid 2020-06-15T22:31:52 prefetch.2.10.7: 1) 'SRR013613' was downloaded successfully Read 6544503 spots for SRR013613/SRR013613.sra Written 6544503 spots for SRR013613/SRR013613.sra 2020-06-15T22:32:19 prefetch.2.10.7: 1) Downloading 'SRR013614'... 2020-06-15T22:32:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:59 prefetch.2.10.7: 'SRR013614' is valid 2020-06-15T22:32:59 prefetch.2.10.7: 1) 'SRR013614' was downloaded successfully Read 6460060 spots for SRR013614/SRR013614.sra Written 6460060 spots for SRR013614/SRR013614.sra 2020-06-15T22:33:26 prefetch.2.10.7: 1) Downloading 'SRR013615'... 2020-06-15T22:33:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:59 prefetch.2.10.7: 'SRR013615' is valid 2020-06-15T22:33:59 prefetch.2.10.7: 1) 'SRR013615' was downloaded successfully Read 6260093 spots for SRR013615/SRR013615.sra Written 6260093 spots for SRR013615/SRR013615.sra 2020-06-15T22:34:25 prefetch.2.10.7: 1) Downloading 'SRR013616'... 2020-06-15T22:34:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:56 prefetch.2.10.7: 'SRR013616' is valid 2020-06-15T22:34:56 prefetch.2.10.7: 1) 'SRR013616' was downloaded successfully Read 5759844 spots for SRR013616/SRR013616.sra Written 5759844 spots for SRR013616/SRR013616.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: 00:02:57 25024500 reads; of these: 25024500 (100.00%) were unpaired; of these: 7641987 (30.54%) aligned 0 times 14738378 (58.90%) aligned exactly 1 time 2644135 (10.57%) aligned >1 times 69.46% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 1629828 / 17382513 = 0.0938 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 07:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.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 07:41:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:01: 1000000 INFO @ Tue, 16 Jun 2020 07:42:06: 2000000 INFO @ Tue, 16 Jun 2020 07:42:11: 3000000 INFO @ Tue, 16 Jun 2020 07:42:16: 4000000 INFO @ Tue, 16 Jun 2020 07:42:21: 5000000 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 07:42:27: 6000000 INFO @ Tue, 16 Jun 2020 07:42:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.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 07:42:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:32: 7000000 INFO @ Tue, 16 Jun 2020 07:42:32: 1000000 INFO @ Tue, 16 Jun 2020 07:42:38: 8000000 INFO @ Tue, 16 Jun 2020 07:42:38: 2000000 INFO @ Tue, 16 Jun 2020 07:42:43: 9000000 INFO @ Tue, 16 Jun 2020 07:42:43: 3000000 INFO @ Tue, 16 Jun 2020 07:42:49: 10000000 INFO @ Tue, 16 Jun 2020 07:42:49: 4000000 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 07:42:54: 11000000 INFO @ Tue, 16 Jun 2020 07:42:54: 5000000 INFO @ Tue, 16 Jun 2020 07:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.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 07:42:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:00: 12000000 INFO @ Tue, 16 Jun 2020 07:43:00: 6000000 INFO @ Tue, 16 Jun 2020 07:43:01: 1000000 INFO @ Tue, 16 Jun 2020 07:43:05: 13000000 INFO @ Tue, 16 Jun 2020 07:43:05: 7000000 INFO @ Tue, 16 Jun 2020 07:43:06: 2000000 INFO @ Tue, 16 Jun 2020 07:43:11: 14000000 INFO @ Tue, 16 Jun 2020 07:43:11: 8000000 INFO @ Tue, 16 Jun 2020 07:43:12: 3000000 INFO @ Tue, 16 Jun 2020 07:43:17: 15000000 INFO @ Tue, 16 Jun 2020 07:43:17: 9000000 INFO @ Tue, 16 Jun 2020 07:43:18: 4000000 INFO @ Tue, 16 Jun 2020 07:43:21: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:43:21: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:43:21: #1 total tags in treatment: 15752685 INFO @ Tue, 16 Jun 2020 07:43:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:21: #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 07:43:21: #1 tags after filtering in treatment: 15752685 INFO @ Tue, 16 Jun 2020 07:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:22: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 07:43:22: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:22: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:43:22: #2 alternative fragment length(s) may be 0,26,58,582 bps INFO @ Tue, 16 Jun 2020 07:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.05_model.r WARNING @ Tue, 16 Jun 2020 07:43:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:43:22: #2 You may need to consider one of the other alternative d(s): 0,26,58,582 WARNING @ Tue, 16 Jun 2020 07:43:22: #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 07:43:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:22: 10000000 INFO @ Tue, 16 Jun 2020 07:43:23: 5000000 INFO @ Tue, 16 Jun 2020 07:43:28: 11000000 INFO @ Tue, 16 Jun 2020 07:43:29: 6000000 INFO @ Tue, 16 Jun 2020 07:43:33: 12000000 INFO @ Tue, 16 Jun 2020 07:43:34: 7000000 INFO @ Tue, 16 Jun 2020 07:43:39: 13000000 INFO @ Tue, 16 Jun 2020 07:43:40: 8000000 INFO @ Tue, 16 Jun 2020 07:43:44: 14000000 INFO @ Tue, 16 Jun 2020 07:43:45: 9000000 INFO @ Tue, 16 Jun 2020 07:43:50: 15000000 INFO @ Tue, 16 Jun 2020 07:43:51: 10000000 INFO @ Tue, 16 Jun 2020 07:43:54: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:43:54: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:43:54: #1 total tags in treatment: 15752685 INFO @ Tue, 16 Jun 2020 07:43:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:54: #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 07:43:54: #1 tags after filtering in treatment: 15752685 INFO @ Tue, 16 Jun 2020 07:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:54: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:56: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 07:43:56: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:56: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:43:56: #2 alternative fragment length(s) may be 0,26,58,582 bps INFO @ Tue, 16 Jun 2020 07:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.10_model.r WARNING @ Tue, 16 Jun 2020 07:43:56: #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 07:43:56: #2 You may need to consider one of the other alternative d(s): 0,26,58,582 WARNING @ Tue, 16 Jun 2020 07:43:56: #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 07:43:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:56: 11000000 INFO @ Tue, 16 Jun 2020 07:44:01: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:07: 13000000 INFO @ Tue, 16 Jun 2020 07:44:12: 14000000 INFO @ Tue, 16 Jun 2020 07:44:17: 15000000 INFO @ Tue, 16 Jun 2020 07:44:21: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:44:21: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:44:21: #1 total tags in treatment: 15752685 INFO @ Tue, 16 Jun 2020 07:44:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:21: #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 07:44:21: #1 tags after filtering in treatment: 15752685 INFO @ Tue, 16 Jun 2020 07:44:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:22: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 07:44:22: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:22: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:44:22: #2 alternative fragment length(s) may be 0,26,58,582 bps INFO @ Tue, 16 Jun 2020 07:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002676/SRX002676.20_model.r WARNING @ Tue, 16 Jun 2020 07:44:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:22: #2 You may need to consider one of the other alternative d(s): 0,26,58,582 WARNING @ Tue, 16 Jun 2020 07:44:22: #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 07:44:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at148/job_scripts/6365849: line 271: 77935 Terminated MACS $i /var/spool/uge/at148/job_scripts/6365849: line 271: 97224 Terminated MACS $i /var/spool/uge/at148/job_scripts/6365849: line 271: 121425 Terminated MACS $i ls: cannot access SRX002676.05.bed: No such file or directory mv: cannot stat ‘SRX002676.05.bed’: No such file or directory mv: cannot stat ‘SRX002676.05.bb’: No such file or directory ls: cannot access SRX002676.10.bed: No such file or directory mv: cannot stat ‘SRX002676.10.bed’: No such file or directory mv: cannot stat ‘SRX002676.10.bb’: No such file or directory ls: cannot access SRX002676.20.bed: No such file or directory mv: cannot stat ‘SRX002676.20.bed’: No such file or directory mv: cannot stat ‘SRX002676.20.bb’: No such file or directory