Job ID = 10165654 SRX = SRX7879261 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24822282 spots for SRR11272876/SRR11272876.sra Written 24822282 spots for SRR11272876/SRR11272876.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165874 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:46 24822282 reads; of these: 24822282 (100.00%) were unpaired; of these: 508103 (2.05%) aligned 0 times 20433446 (82.32%) aligned exactly 1 time 3880733 (15.63%) aligned >1 times 97.95% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 3544668 / 24314179 = 0.1458 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 @ Thu, 08 Oct 2020 19:44:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.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 @ Thu, 08 Oct 2020 19:44:47: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:44:47: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:44:52: 1000000 INFO @ Thu, 08 Oct 2020 19:44:58: 2000000 INFO @ Thu, 08 Oct 2020 19:45:04: 3000000 INFO @ Thu, 08 Oct 2020 19:45:09: 4000000 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 @ Thu, 08 Oct 2020 19:45:15: 5000000 INFO @ Thu, 08 Oct 2020 19:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.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 @ Thu, 08 Oct 2020 19:45:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:45:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:45:21: 6000000 INFO @ Thu, 08 Oct 2020 19:45:23: 1000000 INFO @ Thu, 08 Oct 2020 19:45:27: 7000000 INFO @ Thu, 08 Oct 2020 19:45:29: 2000000 INFO @ Thu, 08 Oct 2020 19:45:33: 8000000 INFO @ Thu, 08 Oct 2020 19:45:35: 3000000 INFO @ Thu, 08 Oct 2020 19:45:39: 9000000 INFO @ Thu, 08 Oct 2020 19:45:41: 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 @ Thu, 08 Oct 2020 19:45:45: 10000000 INFO @ Thu, 08 Oct 2020 19:45:47: 5000000 INFO @ Thu, 08 Oct 2020 19:45:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.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 @ Thu, 08 Oct 2020 19:45:47: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:45:47: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:45:51: 11000000 INFO @ Thu, 08 Oct 2020 19:45:53: 6000000 INFO @ Thu, 08 Oct 2020 19:45:54: 1000000 INFO @ Thu, 08 Oct 2020 19:45:57: 12000000 INFO @ Thu, 08 Oct 2020 19:46:00: 7000000 INFO @ Thu, 08 Oct 2020 19:46:00: 2000000 INFO @ Thu, 08 Oct 2020 19:46:04: 13000000 INFO @ Thu, 08 Oct 2020 19:46:06: 8000000 INFO @ Thu, 08 Oct 2020 19:46:06: 3000000 INFO @ Thu, 08 Oct 2020 19:46:10: 14000000 INFO @ Thu, 08 Oct 2020 19:46:12: 9000000 INFO @ Thu, 08 Oct 2020 19:46:12: 4000000 INFO @ Thu, 08 Oct 2020 19:46:16: 15000000 INFO @ Thu, 08 Oct 2020 19:46:18: 10000000 INFO @ Thu, 08 Oct 2020 19:46:18: 5000000 INFO @ Thu, 08 Oct 2020 19:46:22: 16000000 INFO @ Thu, 08 Oct 2020 19:46:24: 11000000 INFO @ Thu, 08 Oct 2020 19:46:25: 6000000 INFO @ Thu, 08 Oct 2020 19:46:28: 17000000 INFO @ Thu, 08 Oct 2020 19:46:31: 12000000 INFO @ Thu, 08 Oct 2020 19:46:31: 7000000 INFO @ Thu, 08 Oct 2020 19:46:35: 18000000 INFO @ Thu, 08 Oct 2020 19:46:37: 13000000 INFO @ Thu, 08 Oct 2020 19:46:37: 8000000 INFO @ Thu, 08 Oct 2020 19:46:41: 19000000 INFO @ Thu, 08 Oct 2020 19:46:43: 14000000 INFO @ Thu, 08 Oct 2020 19:46:43: 9000000 INFO @ Thu, 08 Oct 2020 19:46:47: 20000000 INFO @ Thu, 08 Oct 2020 19:46:49: 15000000 INFO @ Thu, 08 Oct 2020 19:46:50: 10000000 INFO @ Thu, 08 Oct 2020 19:46:52: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:46:52: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:46:52: #1 total tags in treatment: 20769511 INFO @ Thu, 08 Oct 2020 19:46:52: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:46:52: #1 tags after filtering in treatment: 20769511 INFO @ Thu, 08 Oct 2020 19:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:46:52: #1 finished! INFO @ Thu, 08 Oct 2020 19:46:52: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:46:54: #2 number of paired peaks: 190 WARNING @ Thu, 08 Oct 2020 19:46:54: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Thu, 08 Oct 2020 19:46:54: start model_add_line... INFO @ Thu, 08 Oct 2020 19:46:54: start X-correlation... INFO @ Thu, 08 Oct 2020 19:46:54: end of X-cor INFO @ Thu, 08 Oct 2020 19:46:54: #2 finished! INFO @ Thu, 08 Oct 2020 19:46:54: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 19:46:54: #2 alternative fragment length(s) may be 0,44,508,532 bps INFO @ Thu, 08 Oct 2020 19:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.05_model.r WARNING @ Thu, 08 Oct 2020 19:46:54: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:46:54: #2 You may need to consider one of the other alternative d(s): 0,44,508,532 WARNING @ Thu, 08 Oct 2020 19:46:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:46:54: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:46:56: 16000000 INFO @ Thu, 08 Oct 2020 19:46:56: 11000000 INFO @ Thu, 08 Oct 2020 19:47:02: 17000000 INFO @ Thu, 08 Oct 2020 19:47:02: 12000000 INFO @ Thu, 08 Oct 2020 19:47:08: 18000000 INFO @ Thu, 08 Oct 2020 19:47:08: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:47:14: 19000000 INFO @ Thu, 08 Oct 2020 19:47:14: 14000000 INFO @ Thu, 08 Oct 2020 19:47:21: 20000000 INFO @ Thu, 08 Oct 2020 19:47:21: 15000000 INFO @ Thu, 08 Oct 2020 19:47:25: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:47:25: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:47:25: #1 total tags in treatment: 20769511 INFO @ Thu, 08 Oct 2020 19:47:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:47:26: #1 tags after filtering in treatment: 20769511 INFO @ Thu, 08 Oct 2020 19:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:47:26: #1 finished! INFO @ Thu, 08 Oct 2020 19:47:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:47:27: 16000000 INFO @ Thu, 08 Oct 2020 19:47:27: #2 number of paired peaks: 190 WARNING @ Thu, 08 Oct 2020 19:47:27: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Thu, 08 Oct 2020 19:47:27: start model_add_line... INFO @ Thu, 08 Oct 2020 19:47:27: start X-correlation... INFO @ Thu, 08 Oct 2020 19:47:27: end of X-cor INFO @ Thu, 08 Oct 2020 19:47:27: #2 finished! INFO @ Thu, 08 Oct 2020 19:47:27: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 19:47:27: #2 alternative fragment length(s) may be 0,44,508,532 bps INFO @ Thu, 08 Oct 2020 19:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.10_model.r WARNING @ Thu, 08 Oct 2020 19:47:27: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:47:27: #2 You may need to consider one of the other alternative d(s): 0,44,508,532 WARNING @ Thu, 08 Oct 2020 19:47:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:47:27: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:47:33: 17000000 INFO @ Thu, 08 Oct 2020 19:47:38: 18000000 INFO @ Thu, 08 Oct 2020 19:47:44: 19000000 INFO @ Thu, 08 Oct 2020 19:47:50: 20000000 INFO @ Thu, 08 Oct 2020 19:47:54: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:47:54: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:47:54: #1 total tags in treatment: 20769511 INFO @ Thu, 08 Oct 2020 19:47:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:47:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:47:55: #1 tags after filtering in treatment: 20769511 INFO @ Thu, 08 Oct 2020 19:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:47:55: #1 finished! INFO @ Thu, 08 Oct 2020 19:47:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:47:56: #2 number of paired peaks: 190 WARNING @ Thu, 08 Oct 2020 19:47:56: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Thu, 08 Oct 2020 19:47:56: start model_add_line... INFO @ Thu, 08 Oct 2020 19:47:56: start X-correlation... INFO @ Thu, 08 Oct 2020 19:47:56: end of X-cor INFO @ Thu, 08 Oct 2020 19:47:56: #2 finished! INFO @ Thu, 08 Oct 2020 19:47:56: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 19:47:56: #2 alternative fragment length(s) may be 0,44,508,532 bps INFO @ Thu, 08 Oct 2020 19:47:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879261/SRX7879261.20_model.r WARNING @ Thu, 08 Oct 2020 19:47:56: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:47:56: #2 You may need to consider one of the other alternative d(s): 0,44,508,532 WARNING @ Thu, 08 Oct 2020 19:47:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:47:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:47:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at144/job_scripts/10165654: line 297: 77782 Terminated MACS $i /var/spool/uge/at144/job_scripts/10165654: line 297: 83343 Terminated MACS $i /var/spool/uge/at144/job_scripts/10165654: line 297: 94067 Terminated MACS $i ls: cannot access SRX7879261.05.bed: No such file or directory mv: cannot stat ‘SRX7879261.05.bed’: No such file or directory mv: cannot stat ‘SRX7879261.05.bb’: No such file or directory ls: cannot access SRX7879261.10.bed: No such file or directory mv: cannot stat ‘SRX7879261.10.bed’: No such file or directory mv: cannot stat ‘SRX7879261.10.bb’: No such file or directory ls: cannot access SRX7879261.20.bed: No such file or directory mv: cannot stat ‘SRX7879261.20.bed’: No such file or directory mv: cannot stat ‘SRX7879261.20.bb’: No such file or directory