Job ID = 14160457 SRX = SRX9904326 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14114569 spots for SRR13491812/SRR13491812.sra Written 14114569 spots for SRR13491812/SRR13491812.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160587 ("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: 00:02:48 14114569 reads; of these: 14114569 (100.00%) were unpaired; of these: 3782738 (26.80%) aligned 0 times 8641451 (61.22%) aligned exactly 1 time 1690380 (11.98%) aligned >1 times 73.20% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 1080689 / 10331831 = 0.1046 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 02:42:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.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 02:42:44: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:42:44: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:42:50: 1000000 INFO @ Thu, 09 Dec 2021 02:42:55: 2000000 INFO @ Thu, 09 Dec 2021 02:43:01: 3000000 INFO @ Thu, 09 Dec 2021 02:43:07: 4000000 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 02:43:13: 5000000 INFO @ Thu, 09 Dec 2021 02:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.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 02:43:14: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:43:14: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:43:20: 6000000 INFO @ Thu, 09 Dec 2021 02:43:20: 1000000 INFO @ Thu, 09 Dec 2021 02:43:27: 7000000 INFO @ Thu, 09 Dec 2021 02:43:27: 2000000 INFO @ Thu, 09 Dec 2021 02:43:33: 8000000 INFO @ Thu, 09 Dec 2021 02:43:34: 3000000 INFO @ Thu, 09 Dec 2021 02:43:40: 9000000 INFO @ Thu, 09 Dec 2021 02:43:40: 4000000 INFO @ Thu, 09 Dec 2021 02:43:41: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:43:41: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:43:41: #1 total tags in treatment: 9251142 INFO @ Thu, 09 Dec 2021 02:43:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:43:41: #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 02:43:41: #1 tags after filtering in treatment: 9251142 INFO @ Thu, 09 Dec 2021 02:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:43:41: #1 finished! INFO @ Thu, 09 Dec 2021 02:43:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:43:41: #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 02:43:42: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 02:43:42: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 02:43:42: start model_add_line... INFO @ Thu, 09 Dec 2021 02:43:42: start X-correlation... INFO @ Thu, 09 Dec 2021 02:43:42: end of X-cor INFO @ Thu, 09 Dec 2021 02:43:42: #2 finished! INFO @ Thu, 09 Dec 2021 02:43:42: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 02:43:42: #2 alternative fragment length(s) may be 3,47 bps INFO @ Thu, 09 Dec 2021 02:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.05_model.r WARNING @ Thu, 09 Dec 2021 02:43:42: #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 02:43:42: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Thu, 09 Dec 2021 02:43:42: #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 02:43:42: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:43:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.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 02:43:44: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:43:44: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:43:47: 5000000 INFO @ Thu, 09 Dec 2021 02:43:51: 1000000 INFO @ Thu, 09 Dec 2021 02:43:53: 6000000 INFO @ Thu, 09 Dec 2021 02:43:57: 2000000 INFO @ Thu, 09 Dec 2021 02:44:00: 7000000 INFO @ Thu, 09 Dec 2021 02:44:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:44:04: 3000000 INFO @ Thu, 09 Dec 2021 02:44:07: 8000000 INFO @ Thu, 09 Dec 2021 02:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.05_summits.bed INFO @ Thu, 09 Dec 2021 02:44:10: Done! INFO @ Thu, 09 Dec 2021 02:44:11: 4000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (628 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:44:13: 9000000 INFO @ Thu, 09 Dec 2021 02:44:15: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:44:15: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:44:15: #1 total tags in treatment: 9251142 INFO @ Thu, 09 Dec 2021 02:44:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:44:15: #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 02:44:15: #1 tags after filtering in treatment: 9251142 INFO @ Thu, 09 Dec 2021 02:44:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:44:15: #1 finished! INFO @ Thu, 09 Dec 2021 02:44:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:44:16: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 02:44:16: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 02:44:16: start model_add_line... INFO @ Thu, 09 Dec 2021 02:44:16: start X-correlation... INFO @ Thu, 09 Dec 2021 02:44:16: end of X-cor INFO @ Thu, 09 Dec 2021 02:44:16: #2 finished! INFO @ Thu, 09 Dec 2021 02:44:16: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 02:44:16: #2 alternative fragment length(s) may be 3,47 bps INFO @ Thu, 09 Dec 2021 02:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.10_model.r WARNING @ Thu, 09 Dec 2021 02:44:16: #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 02:44:16: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Thu, 09 Dec 2021 02:44:16: #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 02:44:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:44:17: 5000000 INFO @ Thu, 09 Dec 2021 02:44:24: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:44:29: 7000000 INFO @ Thu, 09 Dec 2021 02:44:34: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:44:35: 8000000 INFO @ Thu, 09 Dec 2021 02:44:41: 9000000 INFO @ Thu, 09 Dec 2021 02:44:42: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:44:42: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:44:42: #1 total tags in treatment: 9251142 INFO @ Thu, 09 Dec 2021 02:44:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:44:42: #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 02:44:43: #1 tags after filtering in treatment: 9251142 INFO @ Thu, 09 Dec 2021 02:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:44:43: #1 finished! INFO @ Thu, 09 Dec 2021 02:44:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:44:43: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 02:44:43: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 02:44:43: start model_add_line... INFO @ Thu, 09 Dec 2021 02:44:43: start X-correlation... INFO @ Thu, 09 Dec 2021 02:44:43: end of X-cor INFO @ Thu, 09 Dec 2021 02:44:43: #2 finished! INFO @ Thu, 09 Dec 2021 02:44:43: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 02:44:43: #2 alternative fragment length(s) may be 3,47 bps INFO @ Thu, 09 Dec 2021 02:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.20_model.r WARNING @ Thu, 09 Dec 2021 02:44:43: #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 02:44:43: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Thu, 09 Dec 2021 02:44:43: #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 02:44:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.10_summits.bed INFO @ Thu, 09 Dec 2021 02:44:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:45:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904326/SRX9904326.20_summits.bed INFO @ Thu, 09 Dec 2021 02:45:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling