Job ID = 6527414 SRX = SRX494956 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:08:05 prefetch.2.10.7: 1) Downloading 'SRR1198488'... 2020-06-29T12:08:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:10:29 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:10:30 prefetch.2.10.7: 'SRR1198488' is valid 2020-06-29T12:10:30 prefetch.2.10.7: 1) 'SRR1198488' was downloaded successfully Read 26663443 spots for SRR1198488/SRR1198488.sra Written 26663443 spots for SRR1198488/SRR1198488.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:06 26663443 reads; of these: 26663443 (100.00%) were unpaired; of these: 3598501 (13.50%) aligned 0 times 18743850 (70.30%) aligned exactly 1 time 4321092 (16.21%) aligned >1 times 86.50% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 3333068 / 23064942 = 0.1445 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 @ Mon, 29 Jun 2020 21:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.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 @ Mon, 29 Jun 2020 21:24:01: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:24:01: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:24:06: 1000000 INFO @ Mon, 29 Jun 2020 21:24:11: 2000000 INFO @ Mon, 29 Jun 2020 21:24:17: 3000000 INFO @ Mon, 29 Jun 2020 21:24:22: 4000000 INFO @ Mon, 29 Jun 2020 21:24:27: 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 @ Mon, 29 Jun 2020 21:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.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 @ Mon, 29 Jun 2020 21:24:31: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:24:31: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:24:32: 6000000 INFO @ Mon, 29 Jun 2020 21:24:37: 1000000 INFO @ Mon, 29 Jun 2020 21:24:38: 7000000 INFO @ Mon, 29 Jun 2020 21:24:43: 2000000 INFO @ Mon, 29 Jun 2020 21:24:44: 8000000 INFO @ Mon, 29 Jun 2020 21:24:48: 3000000 INFO @ Mon, 29 Jun 2020 21:24:50: 9000000 INFO @ Mon, 29 Jun 2020 21:24:54: 4000000 INFO @ Mon, 29 Jun 2020 21:24:56: 10000000 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 @ Mon, 29 Jun 2020 21:25:00: 5000000 INFO @ Mon, 29 Jun 2020 21:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.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 @ Mon, 29 Jun 2020 21:25:01: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:25:01: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:25:02: 11000000 INFO @ Mon, 29 Jun 2020 21:25:06: 6000000 INFO @ Mon, 29 Jun 2020 21:25:07: 1000000 INFO @ Mon, 29 Jun 2020 21:25:08: 12000000 INFO @ Mon, 29 Jun 2020 21:25:12: 7000000 INFO @ Mon, 29 Jun 2020 21:25:13: 2000000 INFO @ Mon, 29 Jun 2020 21:25:14: 13000000 INFO @ Mon, 29 Jun 2020 21:25:18: 8000000 INFO @ Mon, 29 Jun 2020 21:25:19: 3000000 INFO @ Mon, 29 Jun 2020 21:25:20: 14000000 INFO @ Mon, 29 Jun 2020 21:25:24: 9000000 INFO @ Mon, 29 Jun 2020 21:25:25: 4000000 INFO @ Mon, 29 Jun 2020 21:25:26: 15000000 INFO @ Mon, 29 Jun 2020 21:25:29: 10000000 INFO @ Mon, 29 Jun 2020 21:25:31: 5000000 INFO @ Mon, 29 Jun 2020 21:25:32: 16000000 INFO @ Mon, 29 Jun 2020 21:25:35: 11000000 INFO @ Mon, 29 Jun 2020 21:25:37: 6000000 INFO @ Mon, 29 Jun 2020 21:25:38: 17000000 INFO @ Mon, 29 Jun 2020 21:25:41: 12000000 INFO @ Mon, 29 Jun 2020 21:25:43: 7000000 INFO @ Mon, 29 Jun 2020 21:25:44: 18000000 INFO @ Mon, 29 Jun 2020 21:25:47: 13000000 INFO @ Mon, 29 Jun 2020 21:25:49: 8000000 INFO @ Mon, 29 Jun 2020 21:25:50: 19000000 INFO @ Mon, 29 Jun 2020 21:25:53: 14000000 INFO @ Mon, 29 Jun 2020 21:25:54: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:25:54: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:25:54: #1 total tags in treatment: 19731874 INFO @ Mon, 29 Jun 2020 21:25:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:25:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:25:54: #1 tags after filtering in treatment: 19731874 INFO @ Mon, 29 Jun 2020 21:25:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:25:54: #1 finished! INFO @ Mon, 29 Jun 2020 21:25:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:25:55: 9000000 INFO @ Mon, 29 Jun 2020 21:25:56: #2 number of paired peaks: 152 WARNING @ Mon, 29 Jun 2020 21:25:56: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Mon, 29 Jun 2020 21:25:56: start model_add_line... INFO @ Mon, 29 Jun 2020 21:25:56: start X-correlation... INFO @ Mon, 29 Jun 2020 21:25:56: end of X-cor INFO @ Mon, 29 Jun 2020 21:25:56: #2 finished! INFO @ Mon, 29 Jun 2020 21:25:56: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:25:56: #2 alternative fragment length(s) may be 0,31,545,549,559 bps INFO @ Mon, 29 Jun 2020 21:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.05_model.r WARNING @ Mon, 29 Jun 2020 21:25:56: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:25:56: #2 You may need to consider one of the other alternative d(s): 0,31,545,549,559 WARNING @ Mon, 29 Jun 2020 21:25:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:25:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:25:58: 15000000 INFO @ Mon, 29 Jun 2020 21:26:01: 10000000 INFO @ Mon, 29 Jun 2020 21:26:04: 16000000 INFO @ Mon, 29 Jun 2020 21:26:07: 11000000 INFO @ Mon, 29 Jun 2020 21:26:11: 17000000 INFO @ Mon, 29 Jun 2020 21:26:14: 12000000 INFO @ Mon, 29 Jun 2020 21:26:17: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:26:20: 13000000 INFO @ Mon, 29 Jun 2020 21:26:23: 19000000 INFO @ Mon, 29 Jun 2020 21:26:26: 14000000 INFO @ Mon, 29 Jun 2020 21:26:28: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:26:28: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:26:28: #1 total tags in treatment: 19731874 INFO @ Mon, 29 Jun 2020 21:26:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:26:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:26:28: #1 tags after filtering in treatment: 19731874 INFO @ Mon, 29 Jun 2020 21:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:26:28: #1 finished! INFO @ Mon, 29 Jun 2020 21:26:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:26:29: #2 number of paired peaks: 152 WARNING @ Mon, 29 Jun 2020 21:26:29: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Mon, 29 Jun 2020 21:26:29: start model_add_line... INFO @ Mon, 29 Jun 2020 21:26:29: start X-correlation... INFO @ Mon, 29 Jun 2020 21:26:29: end of X-cor INFO @ Mon, 29 Jun 2020 21:26:29: #2 finished! INFO @ Mon, 29 Jun 2020 21:26:29: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:26:29: #2 alternative fragment length(s) may be 0,31,545,549,559 bps INFO @ Mon, 29 Jun 2020 21:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.10_model.r WARNING @ Mon, 29 Jun 2020 21:26:29: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:26:29: #2 You may need to consider one of the other alternative d(s): 0,31,545,549,559 WARNING @ Mon, 29 Jun 2020 21:26:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:26:29: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:26:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:26:32: 15000000 INFO @ Mon, 29 Jun 2020 21:26:37: 16000000 INFO @ Mon, 29 Jun 2020 21:26:43: 17000000 INFO @ Mon, 29 Jun 2020 21:26:48: 18000000 INFO @ Mon, 29 Jun 2020 21:26:53: 19000000 INFO @ Mon, 29 Jun 2020 21:26:57: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:26:57: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:26:57: #1 total tags in treatment: 19731874 INFO @ Mon, 29 Jun 2020 21:26:57: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:26:57: #1 tags after filtering in treatment: 19731874 INFO @ Mon, 29 Jun 2020 21:26:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:26:57: #1 finished! INFO @ Mon, 29 Jun 2020 21:26:57: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:26:59: #2 number of paired peaks: 152 WARNING @ Mon, 29 Jun 2020 21:26:59: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Mon, 29 Jun 2020 21:26:59: start model_add_line... INFO @ Mon, 29 Jun 2020 21:26:59: start X-correlation... INFO @ Mon, 29 Jun 2020 21:26:59: end of X-cor INFO @ Mon, 29 Jun 2020 21:26:59: #2 finished! INFO @ Mon, 29 Jun 2020 21:26:59: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:26:59: #2 alternative fragment length(s) may be 0,31,545,549,559 bps INFO @ Mon, 29 Jun 2020 21:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494956/SRX494956.20_model.r WARNING @ Mon, 29 Jun 2020 21:26:59: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:26:59: #2 You may need to consider one of the other alternative d(s): 0,31,545,549,559 WARNING @ Mon, 29 Jun 2020 21:26:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:26:59: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:26:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at154/job_scripts/6527414: line 293: 37457 Terminated MACS $i /var/spool/uge/at154/job_scripts/6527414: line 293: 37941 Terminated MACS $i /var/spool/uge/at154/job_scripts/6527414: line 293: 38202 Terminated MACS $i ls: cannot access SRX494956.05.bed: No such file or directory mv: cannot stat ‘SRX494956.05.bed’: No such file or directory mv: cannot stat ‘SRX494956.05.bb’: No such file or directory ls: cannot access SRX494956.10.bed: No such file or directory mv: cannot stat ‘SRX494956.10.bed’: No such file or directory mv: cannot stat ‘SRX494956.10.bb’: No such file or directory ls: cannot access SRX494956.20.bed: No such file or directory mv: cannot stat ‘SRX494956.20.bed’: No such file or directory mv: cannot stat ‘SRX494956.20.bb’: No such file or directory