Job ID = 14160530 SRX = SRX8331162 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34618852 spots for SRR11778475/SRR11778475.sra Written 34618852 spots for SRR11778475/SRR11778475.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160677 ("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: 00:10:36 34618852 reads; of these: 34618852 (100.00%) were unpaired; of these: 2947555 (8.51%) aligned 0 times 26086440 (75.35%) aligned exactly 1 time 5584857 (16.13%) aligned >1 times 91.49% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 24496504 / 31671297 = 0.7735 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 @ Thu, 09 Dec 2021 03:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.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, 09 Dec 2021 03:18:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:18:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:18:45: 1000000 INFO @ Thu, 09 Dec 2021 03:18:53: 2000000 INFO @ Thu, 09 Dec 2021 03:19:01: 3000000 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 @ Thu, 09 Dec 2021 03:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.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, 09 Dec 2021 03:19:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:19:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:08: 4000000 INFO @ Thu, 09 Dec 2021 03:19:15: 1000000 INFO @ Thu, 09 Dec 2021 03:19:17: 5000000 INFO @ Thu, 09 Dec 2021 03:19:24: 2000000 INFO @ Thu, 09 Dec 2021 03:19:25: 6000000 INFO @ Thu, 09 Dec 2021 03:19:32: 3000000 INFO @ Thu, 09 Dec 2021 03:19:34: 7000000 INFO @ Thu, 09 Dec 2021 03:19:35: #1 tag size is determined as 68 bps INFO @ Thu, 09 Dec 2021 03:19:35: #1 tag size = 68 INFO @ Thu, 09 Dec 2021 03:19:35: #1 total tags in treatment: 7174793 INFO @ Thu, 09 Dec 2021 03:19:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:19:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:19:35: #1 tags after filtering in treatment: 7174793 INFO @ Thu, 09 Dec 2021 03:19:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:19:35: #1 finished! INFO @ Thu, 09 Dec 2021 03:19:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:19:35: #2 looking for paired plus/minus strand peaks... 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 @ Thu, 09 Dec 2021 03:19:36: #2 number of paired peaks: 824 WARNING @ Thu, 09 Dec 2021 03:19:36: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Thu, 09 Dec 2021 03:19:36: start model_add_line... INFO @ Thu, 09 Dec 2021 03:19:36: start X-correlation... INFO @ Thu, 09 Dec 2021 03:19:36: end of X-cor INFO @ Thu, 09 Dec 2021 03:19:36: #2 finished! INFO @ Thu, 09 Dec 2021 03:19:36: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 03:19:36: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 09 Dec 2021 03:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.05_model.r WARNING @ Thu, 09 Dec 2021 03:19:36: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:19:36: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 09 Dec 2021 03:19:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:19:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.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, 09 Dec 2021 03:19:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:19:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:40: 4000000 INFO @ Thu, 09 Dec 2021 03:19:45: 1000000 INFO @ Thu, 09 Dec 2021 03:19:48: 5000000 INFO @ Thu, 09 Dec 2021 03:19:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:19:52: 2000000 INFO @ Thu, 09 Dec 2021 03:19:56: 6000000 INFO @ Thu, 09 Dec 2021 03:19:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.05_summits.bed INFO @ Thu, 09 Dec 2021 03:19:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1646 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:20:00: 3000000 INFO @ Thu, 09 Dec 2021 03:20:04: 7000000 INFO @ Thu, 09 Dec 2021 03:20:06: #1 tag size is determined as 68 bps INFO @ Thu, 09 Dec 2021 03:20:06: #1 tag size = 68 INFO @ Thu, 09 Dec 2021 03:20:06: #1 total tags in treatment: 7174793 INFO @ Thu, 09 Dec 2021 03:20:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:20:06: #1 tags after filtering in treatment: 7174793 INFO @ Thu, 09 Dec 2021 03:20:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:20:06: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:06: #2 number of paired peaks: 824 WARNING @ Thu, 09 Dec 2021 03:20:06: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:06: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:06: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:06: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:06: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:06: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 03:20:06: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 09 Dec 2021 03:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.10_model.r WARNING @ Thu, 09 Dec 2021 03:20:06: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:06: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 09 Dec 2021 03:20:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:20:06: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:20:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:20:13: 5000000 INFO @ Thu, 09 Dec 2021 03:20:19: 6000000 INFO @ Thu, 09 Dec 2021 03:20:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:20:25: 7000000 INFO @ Thu, 09 Dec 2021 03:20:26: #1 tag size is determined as 68 bps INFO @ Thu, 09 Dec 2021 03:20:26: #1 tag size = 68 INFO @ Thu, 09 Dec 2021 03:20:26: #1 total tags in treatment: 7174793 INFO @ Thu, 09 Dec 2021 03:20:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:20:26: #1 tags after filtering in treatment: 7174793 INFO @ Thu, 09 Dec 2021 03:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:20:26: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:27: #2 number of paired peaks: 824 WARNING @ Thu, 09 Dec 2021 03:20:27: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:27: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 03:20:27: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 09 Dec 2021 03:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.20_model.r WARNING @ Thu, 09 Dec 2021 03:20:27: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:27: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 09 Dec 2021 03:20:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:20:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:20:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:20:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:20:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.10_summits.bed INFO @ Thu, 09 Dec 2021 03:20:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 1283 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:20:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331162/SRX8331162.20_summits.bed INFO @ Thu, 09 Dec 2021 03:20:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 2 millis CompletedMACS2peakCalling