Job ID = 10165679 SRX = SRX8331155 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36309791 spots for SRR11778468/SRR11778468.sra Written 36309791 spots for SRR11778468/SRR11778468.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165981 ("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: 00:12:36 36309791 reads; of these: 36309791 (100.00%) were unpaired; of these: 432164 (1.19%) aligned 0 times 30634592 (84.37%) aligned exactly 1 time 5243035 (14.44%) aligned >1 times 98.81% overall alignment rate Time searching: 00:12:36 Overall time: 00:12:36 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] 16199666 / 35877627 = 0.4515 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 19:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.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 19:56:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:56:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:56:44: 1000000 INFO @ Thu, 08 Oct 2020 19:56:50: 2000000 INFO @ Thu, 08 Oct 2020 19:56:55: 3000000 INFO @ Thu, 08 Oct 2020 19:57:00: 4000000 INFO @ Thu, 08 Oct 2020 19:57:05: 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 @ Thu, 08 Oct 2020 19:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.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 19:57:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:57:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:57:11: 6000000 INFO @ Thu, 08 Oct 2020 19:57:14: 1000000 INFO @ Thu, 08 Oct 2020 19:57:16: 7000000 INFO @ Thu, 08 Oct 2020 19:57:20: 2000000 INFO @ Thu, 08 Oct 2020 19:57:22: 8000000 INFO @ Thu, 08 Oct 2020 19:57:26: 3000000 INFO @ Thu, 08 Oct 2020 19:57:28: 9000000 INFO @ Thu, 08 Oct 2020 19:57:31: 4000000 INFO @ Thu, 08 Oct 2020 19:57:33: 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 @ Thu, 08 Oct 2020 19:57:37: 5000000 INFO @ Thu, 08 Oct 2020 19:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.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 19:57:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:57:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:57:39: 11000000 INFO @ Thu, 08 Oct 2020 19:57:43: 6000000 INFO @ Thu, 08 Oct 2020 19:57:45: 12000000 INFO @ Thu, 08 Oct 2020 19:57:45: 1000000 INFO @ Thu, 08 Oct 2020 19:57:49: 7000000 INFO @ Thu, 08 Oct 2020 19:57:51: 13000000 INFO @ Thu, 08 Oct 2020 19:57:51: 2000000 INFO @ Thu, 08 Oct 2020 19:57:54: 8000000 INFO @ Thu, 08 Oct 2020 19:57:56: 14000000 INFO @ Thu, 08 Oct 2020 19:57:57: 3000000 INFO @ Thu, 08 Oct 2020 19:58:00: 9000000 INFO @ Thu, 08 Oct 2020 19:58:02: 15000000 INFO @ Thu, 08 Oct 2020 19:58:03: 4000000 INFO @ Thu, 08 Oct 2020 19:58:06: 10000000 INFO @ Thu, 08 Oct 2020 19:58:08: 16000000 INFO @ Thu, 08 Oct 2020 19:58:09: 5000000 INFO @ Thu, 08 Oct 2020 19:58:11: 11000000 INFO @ Thu, 08 Oct 2020 19:58:13: 17000000 INFO @ Thu, 08 Oct 2020 19:58:15: 6000000 INFO @ Thu, 08 Oct 2020 19:58:17: 12000000 INFO @ Thu, 08 Oct 2020 19:58:19: 18000000 INFO @ Thu, 08 Oct 2020 19:58:20: 7000000 INFO @ Thu, 08 Oct 2020 19:58:22: 13000000 INFO @ Thu, 08 Oct 2020 19:58:25: 19000000 INFO @ Thu, 08 Oct 2020 19:58:26: 8000000 INFO @ Thu, 08 Oct 2020 19:58:28: 14000000 INFO @ Thu, 08 Oct 2020 19:58:29: #1 tag size is determined as 55 bps INFO @ Thu, 08 Oct 2020 19:58:29: #1 tag size = 55 INFO @ Thu, 08 Oct 2020 19:58:29: #1 total tags in treatment: 19677961 INFO @ Thu, 08 Oct 2020 19:58:29: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:58:29: #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 19:58:29: #1 tags after filtering in treatment: 19677961 INFO @ Thu, 08 Oct 2020 19:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:58:29: #1 finished! INFO @ Thu, 08 Oct 2020 19:58:29: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:58:30: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 19:58:30: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Thu, 08 Oct 2020 19:58:30: start model_add_line... INFO @ Thu, 08 Oct 2020 19:58:31: start X-correlation... INFO @ Thu, 08 Oct 2020 19:58:31: end of X-cor INFO @ Thu, 08 Oct 2020 19:58:31: #2 finished! INFO @ Thu, 08 Oct 2020 19:58:31: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 19:58:31: #2 alternative fragment length(s) may be 2,28,49,52,565 bps INFO @ Thu, 08 Oct 2020 19:58:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.05_model.r WARNING @ Thu, 08 Oct 2020 19:58:31: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:58:31: #2 You may need to consider one of the other alternative d(s): 2,28,49,52,565 WARNING @ Thu, 08 Oct 2020 19:58:31: #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 19:58:31: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:58:32: 9000000 INFO @ Thu, 08 Oct 2020 19:58:34: 15000000 INFO @ Thu, 08 Oct 2020 19:58:38: 10000000 INFO @ Thu, 08 Oct 2020 19:58:39: 16000000 INFO @ Thu, 08 Oct 2020 19:58:43: 11000000 INFO @ Thu, 08 Oct 2020 19:58:45: 17000000 INFO @ Thu, 08 Oct 2020 19:58:49: 12000000 INFO @ Thu, 08 Oct 2020 19:58:50: 18000000 INFO @ Thu, 08 Oct 2020 19:58:55: 13000000 INFO @ Thu, 08 Oct 2020 19:58:56: 19000000 INFO @ Thu, 08 Oct 2020 19:59:00: #1 tag size is determined as 55 bps INFO @ Thu, 08 Oct 2020 19:59:00: #1 tag size = 55 INFO @ Thu, 08 Oct 2020 19:59:00: #1 total tags in treatment: 19677961 INFO @ Thu, 08 Oct 2020 19:59:00: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:59:00: #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 19:59:00: #1 tags after filtering in treatment: 19677961 INFO @ Thu, 08 Oct 2020 19:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:59:00: #1 finished! INFO @ Thu, 08 Oct 2020 19:59:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:59:01: 14000000 INFO @ Thu, 08 Oct 2020 19:59:02: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 19:59:02: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Thu, 08 Oct 2020 19:59:02: start model_add_line... INFO @ Thu, 08 Oct 2020 19:59:02: start X-correlation... INFO @ Thu, 08 Oct 2020 19:59:02: end of X-cor INFO @ Thu, 08 Oct 2020 19:59:02: #2 finished! INFO @ Thu, 08 Oct 2020 19:59:02: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 19:59:02: #2 alternative fragment length(s) may be 2,28,49,52,565 bps INFO @ Thu, 08 Oct 2020 19:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.10_model.r WARNING @ Thu, 08 Oct 2020 19:59:02: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:59:02: #2 You may need to consider one of the other alternative d(s): 2,28,49,52,565 WARNING @ Thu, 08 Oct 2020 19:59:02: #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 19:59:02: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:59:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:59:06: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:59:12: 16000000 INFO @ Thu, 08 Oct 2020 19:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.05_summits.bed INFO @ Thu, 08 Oct 2020 19:59:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:59:17: 17000000 INFO @ Thu, 08 Oct 2020 19:59:23: 18000000 INFO @ Thu, 08 Oct 2020 19:59:28: 19000000 INFO @ Thu, 08 Oct 2020 19:59:32: #1 tag size is determined as 55 bps INFO @ Thu, 08 Oct 2020 19:59:32: #1 tag size = 55 INFO @ Thu, 08 Oct 2020 19:59:32: #1 total tags in treatment: 19677961 INFO @ Thu, 08 Oct 2020 19:59:32: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:59:32: #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 19:59:32: #1 tags after filtering in treatment: 19677961 INFO @ Thu, 08 Oct 2020 19:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:59:32: #1 finished! INFO @ Thu, 08 Oct 2020 19:59:32: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:59:33: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:59:34: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 19:59:34: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Thu, 08 Oct 2020 19:59:34: start model_add_line... INFO @ Thu, 08 Oct 2020 19:59:34: start X-correlation... INFO @ Thu, 08 Oct 2020 19:59:34: end of X-cor INFO @ Thu, 08 Oct 2020 19:59:34: #2 finished! INFO @ Thu, 08 Oct 2020 19:59:34: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 19:59:34: #2 alternative fragment length(s) may be 2,28,49,52,565 bps INFO @ Thu, 08 Oct 2020 19:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.20_model.r WARNING @ Thu, 08 Oct 2020 19:59:34: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:59:34: #2 You may need to consider one of the other alternative d(s): 2,28,49,52,565 WARNING @ Thu, 08 Oct 2020 19:59:34: #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 19:59:34: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:59:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.10_summits.bed INFO @ Thu, 08 Oct 2020 19:59:48: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:00:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331155/SRX8331155.20_summits.bed INFO @ Thu, 08 Oct 2020 20:00:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling