Job ID = 6368241 SRX = SRX494924 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:15:06 prefetch.2.10.7: 1) Downloading 'SRR1198456'... 2020-06-16T00:15:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:20:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:13 prefetch.2.10.7: 1) 'SRR1198456' was downloaded successfully Read 32570721 spots for SRR1198456/SRR1198456.sra Written 32570721 spots for SRR1198456/SRR1198456.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: 00:07:37 32570721 reads; of these: 32570721 (100.00%) were unpaired; of these: 778951 (2.39%) aligned 0 times 25992521 (79.80%) aligned exactly 1 time 5799249 (17.81%) aligned >1 times 97.61% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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 16 files... [bam_rmdupse_core] 5125516 / 31791770 = 0.1612 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 09:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.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 09:37:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:24: 1000000 INFO @ Tue, 16 Jun 2020 09:37:29: 2000000 INFO @ Tue, 16 Jun 2020 09:37:34: 3000000 INFO @ Tue, 16 Jun 2020 09:37:39: 4000000 INFO @ Tue, 16 Jun 2020 09:37:43: 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 09:37:48: 6000000 INFO @ Tue, 16 Jun 2020 09:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.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 09:37:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:53: 7000000 INFO @ Tue, 16 Jun 2020 09:37:54: 1000000 INFO @ Tue, 16 Jun 2020 09:37:58: 8000000 INFO @ Tue, 16 Jun 2020 09:37:59: 2000000 INFO @ Tue, 16 Jun 2020 09:38:02: 9000000 INFO @ Tue, 16 Jun 2020 09:38:04: 3000000 INFO @ Tue, 16 Jun 2020 09:38:07: 10000000 INFO @ Tue, 16 Jun 2020 09:38:09: 4000000 INFO @ Tue, 16 Jun 2020 09:38:12: 11000000 INFO @ Tue, 16 Jun 2020 09:38:14: 5000000 INFO @ Tue, 16 Jun 2020 09:38:17: 12000000 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 09:38:18: 6000000 INFO @ Tue, 16 Jun 2020 09:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.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 09:38:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:22: 13000000 INFO @ Tue, 16 Jun 2020 09:38:23: 7000000 INFO @ Tue, 16 Jun 2020 09:38:24: 1000000 INFO @ Tue, 16 Jun 2020 09:38:26: 14000000 INFO @ Tue, 16 Jun 2020 09:38:28: 8000000 INFO @ Tue, 16 Jun 2020 09:38:29: 2000000 INFO @ Tue, 16 Jun 2020 09:38:31: 15000000 INFO @ Tue, 16 Jun 2020 09:38:33: 9000000 INFO @ Tue, 16 Jun 2020 09:38:34: 3000000 INFO @ Tue, 16 Jun 2020 09:38:36: 16000000 INFO @ Tue, 16 Jun 2020 09:38:38: 10000000 INFO @ Tue, 16 Jun 2020 09:38:39: 4000000 INFO @ Tue, 16 Jun 2020 09:38:41: 17000000 INFO @ Tue, 16 Jun 2020 09:38:43: 11000000 INFO @ Tue, 16 Jun 2020 09:38:45: 5000000 INFO @ Tue, 16 Jun 2020 09:38:46: 18000000 INFO @ Tue, 16 Jun 2020 09:38:48: 12000000 INFO @ Tue, 16 Jun 2020 09:38:50: 6000000 INFO @ Tue, 16 Jun 2020 09:38:51: 19000000 INFO @ Tue, 16 Jun 2020 09:38:53: 13000000 INFO @ Tue, 16 Jun 2020 09:38:55: 7000000 INFO @ Tue, 16 Jun 2020 09:38:56: 20000000 INFO @ Tue, 16 Jun 2020 09:38:58: 14000000 INFO @ Tue, 16 Jun 2020 09:39:00: 8000000 INFO @ Tue, 16 Jun 2020 09:39:01: 21000000 INFO @ Tue, 16 Jun 2020 09:39:03: 15000000 INFO @ Tue, 16 Jun 2020 09:39:05: 9000000 INFO @ Tue, 16 Jun 2020 09:39:07: 22000000 INFO @ Tue, 16 Jun 2020 09:39:08: 16000000 INFO @ Tue, 16 Jun 2020 09:39:10: 10000000 INFO @ Tue, 16 Jun 2020 09:39:12: 23000000 INFO @ Tue, 16 Jun 2020 09:39:13: 17000000 INFO @ Tue, 16 Jun 2020 09:39:15: 11000000 INFO @ Tue, 16 Jun 2020 09:39:17: 24000000 INFO @ Tue, 16 Jun 2020 09:39:18: 18000000 INFO @ Tue, 16 Jun 2020 09:39:20: 12000000 INFO @ Tue, 16 Jun 2020 09:39:22: 25000000 INFO @ Tue, 16 Jun 2020 09:39:23: 19000000 INFO @ Tue, 16 Jun 2020 09:39:25: 13000000 INFO @ Tue, 16 Jun 2020 09:39:27: 26000000 INFO @ Tue, 16 Jun 2020 09:39:29: 20000000 INFO @ Tue, 16 Jun 2020 09:39:30: 14000000 INFO @ Tue, 16 Jun 2020 09:39:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:30: #1 total tags in treatment: 26666254 INFO @ Tue, 16 Jun 2020 09:39:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:30: #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 09:39:31: #1 tags after filtering in treatment: 26666254 INFO @ Tue, 16 Jun 2020 09:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:33: #2 number of paired peaks: 124 WARNING @ Tue, 16 Jun 2020 09:39:33: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:33: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:39:33: #2 alternative fragment length(s) may be 0,45,184,449,521,576 bps INFO @ Tue, 16 Jun 2020 09:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.05_model.r WARNING @ Tue, 16 Jun 2020 09:39:33: #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 09:39:33: #2 You may need to consider one of the other alternative d(s): 0,45,184,449,521,576 WARNING @ Tue, 16 Jun 2020 09:39:33: #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 09:39:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:34: 21000000 INFO @ Tue, 16 Jun 2020 09:39:35: 15000000 INFO @ Tue, 16 Jun 2020 09:39:39: 22000000 INFO @ Tue, 16 Jun 2020 09:39:40: 16000000 INFO @ Tue, 16 Jun 2020 09:39:44: 23000000 INFO @ Tue, 16 Jun 2020 09:39:46: 17000000 INFO @ Tue, 16 Jun 2020 09:39:49: 24000000 INFO @ Tue, 16 Jun 2020 09:39:51: 18000000 INFO @ Tue, 16 Jun 2020 09:39:54: 25000000 INFO @ Tue, 16 Jun 2020 09:39:56: 19000000 INFO @ Tue, 16 Jun 2020 09:39:59: 26000000 INFO @ Tue, 16 Jun 2020 09:40:01: 20000000 INFO @ Tue, 16 Jun 2020 09:40:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:03: #1 total tags in treatment: 26666254 INFO @ Tue, 16 Jun 2020 09:40:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:03: #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 09:40:03: #1 tags after filtering in treatment: 26666254 INFO @ Tue, 16 Jun 2020 09:40:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:05: #2 number of paired peaks: 124 WARNING @ Tue, 16 Jun 2020 09:40:05: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:05: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:40:05: #2 alternative fragment length(s) may be 0,45,184,449,521,576 bps INFO @ Tue, 16 Jun 2020 09:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.10_model.r WARNING @ Tue, 16 Jun 2020 09:40:05: #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 09:40:05: #2 You may need to consider one of the other alternative d(s): 0,45,184,449,521,576 WARNING @ Tue, 16 Jun 2020 09:40:05: #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 09:40:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:06: 21000000 INFO @ Tue, 16 Jun 2020 09:40:11: 22000000 INFO @ Tue, 16 Jun 2020 09:40:16: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:22: 24000000 INFO @ Tue, 16 Jun 2020 09:40:27: 25000000 INFO @ Tue, 16 Jun 2020 09:40:32: 26000000 INFO @ Tue, 16 Jun 2020 09:40:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:35: #1 total tags in treatment: 26666254 INFO @ Tue, 16 Jun 2020 09:40:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:35: #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 09:40:36: #1 tags after filtering in treatment: 26666254 INFO @ Tue, 16 Jun 2020 09:40:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:38: #2 number of paired peaks: 124 WARNING @ Tue, 16 Jun 2020 09:40:38: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:38: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:40:38: #2 alternative fragment length(s) may be 0,45,184,449,521,576 bps INFO @ Tue, 16 Jun 2020 09:40:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494924/SRX494924.20_model.r WARNING @ Tue, 16 Jun 2020 09:40:38: #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 09:40:38: #2 You may need to consider one of the other alternative d(s): 0,45,184,449,521,576 WARNING @ Tue, 16 Jun 2020 09:40:38: #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 09:40:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at140/job_scripts/6368241: line 271: 22847 Terminated MACS $i /var/spool/uge/at140/job_scripts/6368241: line 271: 37672 Terminated MACS $i /var/spool/uge/at140/job_scripts/6368241: line 271: 38243 Terminated MACS $i ls: cannot access SRX494924.05.bed: No such file or directory mv: cannot stat ‘SRX494924.05.bed’: No such file or directory mv: cannot stat ‘SRX494924.05.bb’: No such file or directory ls: cannot access SRX494924.10.bed: No such file or directory mv: cannot stat ‘SRX494924.10.bed’: No such file or directory mv: cannot stat ‘SRX494924.10.bb’: No such file or directory ls: cannot access SRX494924.20.bed: No such file or directory mv: cannot stat ‘SRX494924.20.bed’: No such file or directory mv: cannot stat ‘SRX494924.20.bb’: No such file or directory