Job ID = 6368041 SRX = SRX466504 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:18 prefetch.2.10.7: 1) Downloading 'SRR1163570'... 2020-06-16T00:24:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:26 prefetch.2.10.7: 1) 'SRR1163570' was downloaded successfully Read 30788149 spots for SRR1163570/SRR1163570.sra Written 30788149 spots for SRR1163570/SRR1163570.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: 00:05:11 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169813 (0.55%) aligned 0 times 25275374 (82.09%) aligned exactly 1 time 5342962 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 4711318 / 30618336 = 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 09:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.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 09:40:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:34: 1000000 INFO @ Tue, 16 Jun 2020 09:40:39: 2000000 INFO @ Tue, 16 Jun 2020 09:40:44: 3000000 INFO @ Tue, 16 Jun 2020 09:40:49: 4000000 INFO @ Tue, 16 Jun 2020 09:40:54: 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 09:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.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 09:40:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:00: 6000000 INFO @ Tue, 16 Jun 2020 09:41:05: 1000000 INFO @ Tue, 16 Jun 2020 09:41:06: 7000000 INFO @ Tue, 16 Jun 2020 09:41:11: 8000000 INFO @ Tue, 16 Jun 2020 09:41:12: 2000000 INFO @ Tue, 16 Jun 2020 09:41:17: 9000000 INFO @ Tue, 16 Jun 2020 09:41:18: 3000000 INFO @ Tue, 16 Jun 2020 09:41:23: 10000000 INFO @ Tue, 16 Jun 2020 09:41:25: 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 09:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.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 09:41:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:29: 11000000 INFO @ Tue, 16 Jun 2020 09:41:32: 5000000 INFO @ Tue, 16 Jun 2020 09:41:35: 1000000 INFO @ Tue, 16 Jun 2020 09:41:35: 12000000 INFO @ Tue, 16 Jun 2020 09:41:39: 6000000 INFO @ Tue, 16 Jun 2020 09:41:41: 2000000 INFO @ Tue, 16 Jun 2020 09:41:41: 13000000 INFO @ Tue, 16 Jun 2020 09:41:46: 7000000 INFO @ Tue, 16 Jun 2020 09:41:47: 3000000 INFO @ Tue, 16 Jun 2020 09:41:47: 14000000 INFO @ Tue, 16 Jun 2020 09:41:52: 8000000 INFO @ Tue, 16 Jun 2020 09:41:53: 4000000 INFO @ Tue, 16 Jun 2020 09:41:54: 15000000 INFO @ Tue, 16 Jun 2020 09:41:59: 9000000 INFO @ Tue, 16 Jun 2020 09:42:00: 16000000 INFO @ Tue, 16 Jun 2020 09:42:00: 5000000 INFO @ Tue, 16 Jun 2020 09:42:05: 10000000 INFO @ Tue, 16 Jun 2020 09:42:06: 17000000 INFO @ Tue, 16 Jun 2020 09:42:06: 6000000 INFO @ Tue, 16 Jun 2020 09:42:12: 11000000 INFO @ Tue, 16 Jun 2020 09:42:12: 18000000 INFO @ Tue, 16 Jun 2020 09:42:12: 7000000 INFO @ Tue, 16 Jun 2020 09:42:18: 19000000 INFO @ Tue, 16 Jun 2020 09:42:19: 12000000 INFO @ Tue, 16 Jun 2020 09:42:19: 8000000 INFO @ Tue, 16 Jun 2020 09:42:24: 20000000 INFO @ Tue, 16 Jun 2020 09:42:25: 9000000 INFO @ Tue, 16 Jun 2020 09:42:25: 13000000 INFO @ Tue, 16 Jun 2020 09:42:30: 21000000 INFO @ Tue, 16 Jun 2020 09:42:31: 10000000 INFO @ Tue, 16 Jun 2020 09:42:32: 14000000 INFO @ Tue, 16 Jun 2020 09:42:36: 22000000 INFO @ Tue, 16 Jun 2020 09:42:37: 11000000 INFO @ Tue, 16 Jun 2020 09:42:39: 15000000 INFO @ Tue, 16 Jun 2020 09:42:42: 23000000 INFO @ Tue, 16 Jun 2020 09:42:43: 12000000 INFO @ Tue, 16 Jun 2020 09:42:45: 16000000 INFO @ Tue, 16 Jun 2020 09:42:48: 24000000 INFO @ Tue, 16 Jun 2020 09:42:49: 13000000 INFO @ Tue, 16 Jun 2020 09:42:52: 17000000 INFO @ Tue, 16 Jun 2020 09:42:54: 25000000 INFO @ Tue, 16 Jun 2020 09:42:55: 14000000 INFO @ Tue, 16 Jun 2020 09:42:58: 18000000 INFO @ Tue, 16 Jun 2020 09:42:59: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:42:59: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:42:59: #1 total tags in treatment: 25907018 INFO @ Tue, 16 Jun 2020 09:42:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:59: #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 09:43:00: #1 tags after filtering in treatment: 25907018 INFO @ Tue, 16 Jun 2020 09:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:01: 15000000 INFO @ Tue, 16 Jun 2020 09:43:01: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 09:43:01: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:02: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:43:02: #2 alternative fragment length(s) may be 0,31,167,293,311,388,445,534 bps INFO @ Tue, 16 Jun 2020 09:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.05_model.r WARNING @ Tue, 16 Jun 2020 09:43:02: #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 09:43:02: #2 You may need to consider one of the other alternative d(s): 0,31,167,293,311,388,445,534 WARNING @ Tue, 16 Jun 2020 09:43:02: #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 09:43:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:05: 19000000 INFO @ Tue, 16 Jun 2020 09:43:06: 16000000 INFO @ Tue, 16 Jun 2020 09:43:11: 20000000 INFO @ Tue, 16 Jun 2020 09:43:12: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:17: 21000000 INFO @ Tue, 16 Jun 2020 09:43:18: 18000000 INFO @ Tue, 16 Jun 2020 09:43:24: 19000000 INFO @ Tue, 16 Jun 2020 09:43:24: 22000000 INFO @ Tue, 16 Jun 2020 09:43:29: 20000000 INFO @ Tue, 16 Jun 2020 09:43:30: 23000000 INFO @ Tue, 16 Jun 2020 09:43:35: 21000000 INFO @ Tue, 16 Jun 2020 09:43:36: 24000000 INFO @ Tue, 16 Jun 2020 09:43:41: 22000000 INFO @ Tue, 16 Jun 2020 09:43:42: 25000000 INFO @ Tue, 16 Jun 2020 09:43:47: 23000000 INFO @ Tue, 16 Jun 2020 09:43:47: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:43:47: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:43:47: #1 total tags in treatment: 25907018 INFO @ Tue, 16 Jun 2020 09:43:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:47: #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 09:43:48: #1 tags after filtering in treatment: 25907018 INFO @ Tue, 16 Jun 2020 09:43:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:49: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 09:43:49: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:50: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:43:50: #2 alternative fragment length(s) may be 0,31,167,293,311,388,445,534 bps INFO @ Tue, 16 Jun 2020 09:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:50: #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 09:43:50: #2 You may need to consider one of the other alternative d(s): 0,31,167,293,311,388,445,534 WARNING @ Tue, 16 Jun 2020 09:43:50: #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 09:43:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:52: 24000000 INFO @ Tue, 16 Jun 2020 09:43:57: 25000000 INFO @ Tue, 16 Jun 2020 09:44:02: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:44:02: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:44:02: #1 total tags in treatment: 25907018 INFO @ Tue, 16 Jun 2020 09:44:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:02: #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 09:44:02: #1 tags after filtering in treatment: 25907018 INFO @ Tue, 16 Jun 2020 09:44:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:04: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 09:44:04: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:04: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:44:04: #2 alternative fragment length(s) may be 0,31,167,293,311,388,445,534 bps INFO @ Tue, 16 Jun 2020 09:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466504/SRX466504.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:04: #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 09:44:04: #2 You may need to consider one of the other alternative d(s): 0,31,167,293,311,388,445,534 WARNING @ Tue, 16 Jun 2020 09:44:04: #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 09:44:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at149/job_scripts/6368041: line 271: 108466 Terminated MACS $i /var/spool/uge/at149/job_scripts/6368041: line 271: 7537 Terminated MACS $i /var/spool/uge/at149/job_scripts/6368041: line 271: 20831 Terminated MACS $i ls: cannot access SRX466504.05.bed: No such file or directory mv: cannot stat ‘SRX466504.05.bed’: No such file or directory mv: cannot stat ‘SRX466504.05.bb’: No such file or directory ls: cannot access SRX466504.10.bed: No such file or directory mv: cannot stat ‘SRX466504.10.bed’: No such file or directory mv: cannot stat ‘SRX466504.10.bb’: No such file or directory ls: cannot access SRX466504.20.bed: No such file or directory mv: cannot stat ‘SRX466504.20.bed’: No such file or directory mv: cannot stat ‘SRX466504.20.bb’: No such file or directory