Job ID = 14158255 SRX = SRX7739523 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14396999 spots for SRR11100927/SRR11100927.sra Written 14396999 spots for SRR11100927/SRR11100927.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158767 ("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: 00:02:35 14396999 reads; of these: 14396999 (100.00%) were unpaired; of these: 6472111 (44.95%) aligned 0 times 6613546 (45.94%) aligned exactly 1 time 1311342 (9.11%) aligned >1 times 55.05% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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_rmdupse_core] 1337234 / 7924888 = 0.1687 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.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 @ Wed, 08 Dec 2021 15:27:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:27:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:27:27: 1000000 INFO @ Wed, 08 Dec 2021 15:27:32: 2000000 INFO @ Wed, 08 Dec 2021 15:27:37: 3000000 INFO @ Wed, 08 Dec 2021 15:27:42: 4000000 INFO @ Wed, 08 Dec 2021 15:27:47: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.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 @ Wed, 08 Dec 2021 15:27:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:27:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:27:52: 6000000 INFO @ Wed, 08 Dec 2021 15:27:56: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:27:56: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:27:56: #1 total tags in treatment: 6587654 INFO @ Wed, 08 Dec 2021 15:27:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:27:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:27:56: #1 tags after filtering in treatment: 6587654 INFO @ Wed, 08 Dec 2021 15:27:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:27:56: #1 finished! INFO @ Wed, 08 Dec 2021 15:27:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:27:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:27:56: #2 number of paired peaks: 392 WARNING @ Wed, 08 Dec 2021 15:27:56: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 08 Dec 2021 15:27:56: start model_add_line... INFO @ Wed, 08 Dec 2021 15:27:56: start X-correlation... INFO @ Wed, 08 Dec 2021 15:27:56: end of X-cor INFO @ Wed, 08 Dec 2021 15:27:56: #2 finished! INFO @ Wed, 08 Dec 2021 15:27:56: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 15:27:56: #2 alternative fragment length(s) may be 3,49,502 bps INFO @ Wed, 08 Dec 2021 15:27:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.05_model.r WARNING @ Wed, 08 Dec 2021 15:27:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:27:56: #2 You may need to consider one of the other alternative d(s): 3,49,502 WARNING @ Wed, 08 Dec 2021 15:27:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:27:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:27:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:27:57: 1000000 INFO @ Wed, 08 Dec 2021 15:28:02: 2000000 INFO @ Wed, 08 Dec 2021 15:28:07: 3000000 INFO @ Wed, 08 Dec 2021 15:28:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:28:13: 4000000 INFO @ Wed, 08 Dec 2021 15:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.05_summits.bed INFO @ Wed, 08 Dec 2021 15:28:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 71 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:28:18: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:28:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.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 @ Wed, 08 Dec 2021 15:28:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:28:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:28:23: 6000000 INFO @ Wed, 08 Dec 2021 15:28:26: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:28:26: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:28:26: #1 total tags in treatment: 6587654 INFO @ Wed, 08 Dec 2021 15:28:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:28:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:28:27: #1 tags after filtering in treatment: 6587654 INFO @ Wed, 08 Dec 2021 15:28:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:28:27: #1 finished! INFO @ Wed, 08 Dec 2021 15:28:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:28:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:28:27: 1000000 INFO @ Wed, 08 Dec 2021 15:28:27: #2 number of paired peaks: 392 WARNING @ Wed, 08 Dec 2021 15:28:27: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 08 Dec 2021 15:28:27: start model_add_line... INFO @ Wed, 08 Dec 2021 15:28:27: start X-correlation... INFO @ Wed, 08 Dec 2021 15:28:27: end of X-cor INFO @ Wed, 08 Dec 2021 15:28:27: #2 finished! INFO @ Wed, 08 Dec 2021 15:28:27: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 15:28:27: #2 alternative fragment length(s) may be 3,49,502 bps INFO @ Wed, 08 Dec 2021 15:28:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.10_model.r WARNING @ Wed, 08 Dec 2021 15:28:27: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:28:27: #2 You may need to consider one of the other alternative d(s): 3,49,502 WARNING @ Wed, 08 Dec 2021 15:28:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:28:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:28:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:28:33: 2000000 INFO @ Wed, 08 Dec 2021 15:28:38: 3000000 INFO @ Wed, 08 Dec 2021 15:28:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:28:44: 4000000 INFO @ Wed, 08 Dec 2021 15:28:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:28:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:28:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.10_summits.bed INFO @ Wed, 08 Dec 2021 15:28:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (371 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:28:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:28:54: 6000000 INFO @ Wed, 08 Dec 2021 15:28:57: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:28:57: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:28:57: #1 total tags in treatment: 6587654 INFO @ Wed, 08 Dec 2021 15:28:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:28:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:28:57: #1 tags after filtering in treatment: 6587654 INFO @ Wed, 08 Dec 2021 15:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:28:57: #1 finished! INFO @ Wed, 08 Dec 2021 15:28:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:28:58: #2 number of paired peaks: 392 WARNING @ Wed, 08 Dec 2021 15:28:58: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 08 Dec 2021 15:28:58: start model_add_line... INFO @ Wed, 08 Dec 2021 15:28:58: start X-correlation... INFO @ Wed, 08 Dec 2021 15:28:58: end of X-cor INFO @ Wed, 08 Dec 2021 15:28:58: #2 finished! INFO @ Wed, 08 Dec 2021 15:28:58: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 15:28:58: #2 alternative fragment length(s) may be 3,49,502 bps INFO @ Wed, 08 Dec 2021 15:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.20_model.r WARNING @ Wed, 08 Dec 2021 15:28:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:28:58: #2 You may need to consider one of the other alternative d(s): 3,49,502 WARNING @ Wed, 08 Dec 2021 15:28:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:28:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:28:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:29:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739523/SRX7739523.20_summits.bed INFO @ Wed, 08 Dec 2021 15:29:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 millis CompletedMACS2peakCalling