Job ID = 14160520 SRX = SRX8151889 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:33 19857573 reads; of these: 19857573 (100.00%) were unpaired; of these: 1542312 (7.77%) aligned 0 times 15282051 (76.96%) aligned exactly 1 time 3033210 (15.27%) aligned >1 times 92.23% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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 8 files... [bam_rmdupse_core] 1588601 / 18315261 = 0.0867 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 03:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.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 03:04:38: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:04:38: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:04:42: 1000000 INFO @ Thu, 09 Dec 2021 03:04:47: 2000000 INFO @ Thu, 09 Dec 2021 03:04:51: 3000000 INFO @ Thu, 09 Dec 2021 03:04:56: 4000000 INFO @ Thu, 09 Dec 2021 03:05:00: 5000000 INFO @ Thu, 09 Dec 2021 03:05:05: 6000000 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 03:05:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.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 03:05:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:05:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:05:10: 7000000 INFO @ Thu, 09 Dec 2021 03:05:12: 1000000 INFO @ Thu, 09 Dec 2021 03:05:15: 8000000 INFO @ Thu, 09 Dec 2021 03:05:17: 2000000 INFO @ Thu, 09 Dec 2021 03:05:19: 9000000 INFO @ Thu, 09 Dec 2021 03:05:21: 3000000 INFO @ Thu, 09 Dec 2021 03:05:24: 10000000 INFO @ Thu, 09 Dec 2021 03:05:26: 4000000 INFO @ Thu, 09 Dec 2021 03:05:29: 11000000 INFO @ Thu, 09 Dec 2021 03:05:31: 5000000 INFO @ Thu, 09 Dec 2021 03:05:33: 12000000 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 03:05:36: 6000000 INFO @ Thu, 09 Dec 2021 03:05:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.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 03:05:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:05:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:05:38: 13000000 INFO @ Thu, 09 Dec 2021 03:05:41: 7000000 INFO @ Thu, 09 Dec 2021 03:05:42: 1000000 INFO @ Thu, 09 Dec 2021 03:05:43: 14000000 INFO @ Thu, 09 Dec 2021 03:05:46: 8000000 INFO @ Thu, 09 Dec 2021 03:05:47: 2000000 INFO @ Thu, 09 Dec 2021 03:05:47: 15000000 INFO @ Thu, 09 Dec 2021 03:05:51: 9000000 INFO @ Thu, 09 Dec 2021 03:05:51: 3000000 INFO @ Thu, 09 Dec 2021 03:05:52: 16000000 INFO @ Thu, 09 Dec 2021 03:05:55: 10000000 INFO @ Thu, 09 Dec 2021 03:05:55: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:05:55: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:05:55: #1 total tags in treatment: 16726660 INFO @ Thu, 09 Dec 2021 03:05:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:05:55: #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 03:05:56: #1 tags after filtering in treatment: 16726660 INFO @ Thu, 09 Dec 2021 03:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:05:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:05:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:05:56: 4000000 INFO @ Thu, 09 Dec 2021 03:05:57: #2 number of paired peaks: 211 WARNING @ Thu, 09 Dec 2021 03:05:57: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 09 Dec 2021 03:05:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:05:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:05:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:05:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:05:57: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 03:05:57: #2 alternative fragment length(s) may be 1,47,507,550 bps INFO @ Thu, 09 Dec 2021 03:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.05_model.r WARNING @ Thu, 09 Dec 2021 03:05:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:05:57: #2 You may need to consider one of the other alternative d(s): 1,47,507,550 WARNING @ Thu, 09 Dec 2021 03:05:57: #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 03:05:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:06:00: 11000000 INFO @ Thu, 09 Dec 2021 03:06:01: 5000000 INFO @ Thu, 09 Dec 2021 03:06:04: 12000000 INFO @ Thu, 09 Dec 2021 03:06:06: 6000000 INFO @ Thu, 09 Dec 2021 03:06:09: 13000000 INFO @ Thu, 09 Dec 2021 03:06:11: 7000000 INFO @ Thu, 09 Dec 2021 03:06:14: 14000000 INFO @ Thu, 09 Dec 2021 03:06:16: 8000000 INFO @ Thu, 09 Dec 2021 03:06:18: 15000000 INFO @ Thu, 09 Dec 2021 03:06:20: 9000000 INFO @ Thu, 09 Dec 2021 03:06:23: 16000000 INFO @ Thu, 09 Dec 2021 03:06:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:06:25: 10000000 INFO @ Thu, 09 Dec 2021 03:06:26: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:06:26: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:06:26: #1 total tags in treatment: 16726660 INFO @ Thu, 09 Dec 2021 03:06:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:06:26: #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 03:06:27: #1 tags after filtering in treatment: 16726660 INFO @ Thu, 09 Dec 2021 03:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:06:27: #1 finished! INFO @ Thu, 09 Dec 2021 03:06:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:06:28: #2 number of paired peaks: 211 WARNING @ Thu, 09 Dec 2021 03:06:28: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 09 Dec 2021 03:06:28: start model_add_line... INFO @ Thu, 09 Dec 2021 03:06:28: start X-correlation... INFO @ Thu, 09 Dec 2021 03:06:28: end of X-cor INFO @ Thu, 09 Dec 2021 03:06:28: #2 finished! INFO @ Thu, 09 Dec 2021 03:06:28: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 03:06:28: #2 alternative fragment length(s) may be 1,47,507,550 bps INFO @ Thu, 09 Dec 2021 03:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.10_model.r WARNING @ Thu, 09 Dec 2021 03:06:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:06:28: #2 You may need to consider one of the other alternative d(s): 1,47,507,550 WARNING @ Thu, 09 Dec 2021 03:06:28: #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 03:06:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:06:29: 11000000 INFO @ Thu, 09 Dec 2021 03:06:34: 12000000 INFO @ Thu, 09 Dec 2021 03:06:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:06:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:06:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.05_summits.bed INFO @ Thu, 09 Dec 2021 03:06:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:06:39: 13000000 INFO @ Thu, 09 Dec 2021 03:06:43: 14000000 INFO @ Thu, 09 Dec 2021 03:06:48: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:06:52: 16000000 INFO @ Thu, 09 Dec 2021 03:06:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:06:56: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:06:56: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:06:56: #1 total tags in treatment: 16726660 INFO @ Thu, 09 Dec 2021 03:06:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:06:56: #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 03:06:56: #1 tags after filtering in treatment: 16726660 INFO @ Thu, 09 Dec 2021 03:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:06:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:06:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:06:57: #2 number of paired peaks: 211 WARNING @ Thu, 09 Dec 2021 03:06:57: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 09 Dec 2021 03:06:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:06:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:06:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:06:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:06:57: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 03:06:57: #2 alternative fragment length(s) may be 1,47,507,550 bps INFO @ Thu, 09 Dec 2021 03:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.20_model.r WARNING @ Thu, 09 Dec 2021 03:06:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:06:57: #2 You may need to consider one of the other alternative d(s): 1,47,507,550 WARNING @ Thu, 09 Dec 2021 03:06:57: #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 03:06:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:07:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:07:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.10_summits.bed INFO @ Thu, 09 Dec 2021 03:07:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:07:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8151889/SRX8151889.20_summits.bed INFO @ Thu, 09 Dec 2021 03:07:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling