Job ID = 14160722 SRX = SRX10569208 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:53:13 prefetch.2.10.7: 1) Downloading 'SRR14202284'... 2021-12-08T18:53:13 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:56:18 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:56:18 prefetch.2.10.7: 1) 'SRR14202284' was downloaded successfully 2021-12-08T18:56:18 prefetch.2.10.7: 'SRR14202284' has 0 unresolved dependencies Read 18447727 spots for SRR14202284/SRR14202284.sra Written 18447727 spots for SRR14202284/SRR14202284.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160851 ("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: 00:05:06 18447727 reads; of these: 18447727 (100.00%) were unpaired; of these: 9095045 (49.30%) aligned 0 times 7427827 (40.26%) aligned exactly 1 time 1924855 (10.43%) aligned >1 times 50.70% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 1747152 / 9352682 = 0.1868 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 04:05:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.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 04:05:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:05:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:05:43: 1000000 INFO @ Thu, 09 Dec 2021 04:05:48: 2000000 INFO @ Thu, 09 Dec 2021 04:05:54: 3000000 INFO @ Thu, 09 Dec 2021 04:05:59: 4000000 INFO @ Thu, 09 Dec 2021 04:06:05: 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 @ Thu, 09 Dec 2021 04:06:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.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 04:06:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:06:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:06:11: 6000000 INFO @ Thu, 09 Dec 2021 04:06:14: 1000000 INFO @ Thu, 09 Dec 2021 04:06:17: 7000000 INFO @ Thu, 09 Dec 2021 04:06:20: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:06:20: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:06:20: #1 total tags in treatment: 7605530 INFO @ Thu, 09 Dec 2021 04:06:20: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:06:20: #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 04:06:20: #1 tags after filtering in treatment: 7605530 INFO @ Thu, 09 Dec 2021 04:06:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:06:20: #1 finished! INFO @ Thu, 09 Dec 2021 04:06:20: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:06:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:06:21: #2 number of paired peaks: 422 WARNING @ Thu, 09 Dec 2021 04:06:21: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Thu, 09 Dec 2021 04:06:21: start model_add_line... INFO @ Thu, 09 Dec 2021 04:06:21: start X-correlation... INFO @ Thu, 09 Dec 2021 04:06:21: end of X-cor INFO @ Thu, 09 Dec 2021 04:06:21: #2 finished! INFO @ Thu, 09 Dec 2021 04:06:21: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:06:21: #2 alternative fragment length(s) may be 4,60,571 bps INFO @ Thu, 09 Dec 2021 04:06:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.05_model.r WARNING @ Thu, 09 Dec 2021 04:06:21: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:06:21: #2 You may need to consider one of the other alternative d(s): 4,60,571 WARNING @ Thu, 09 Dec 2021 04:06:21: #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 04:06:21: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:06:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:06:21: 2000000 INFO @ Thu, 09 Dec 2021 04:06:28: 3000000 INFO @ Thu, 09 Dec 2021 04:06:34: 4000000 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 04:06:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.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 04:06:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:06:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:06:41: 5000000 INFO @ Thu, 09 Dec 2021 04:06:43: 1000000 INFO @ Thu, 09 Dec 2021 04:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.05_summits.bed INFO @ Thu, 09 Dec 2021 04:06:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (607 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:06:48: 6000000 INFO @ Thu, 09 Dec 2021 04:06:49: 2000000 INFO @ Thu, 09 Dec 2021 04:06:55: 7000000 INFO @ Thu, 09 Dec 2021 04:06:55: 3000000 INFO @ Thu, 09 Dec 2021 04:06:59: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:06:59: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:06:59: #1 total tags in treatment: 7605530 INFO @ Thu, 09 Dec 2021 04:06:59: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:06:59: #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 04:06:59: #1 tags after filtering in treatment: 7605530 INFO @ Thu, 09 Dec 2021 04:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:06:59: #1 finished! INFO @ Thu, 09 Dec 2021 04:06:59: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:07:00: #2 number of paired peaks: 422 WARNING @ Thu, 09 Dec 2021 04:07:00: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Thu, 09 Dec 2021 04:07:00: start model_add_line... INFO @ Thu, 09 Dec 2021 04:07:00: start X-correlation... INFO @ Thu, 09 Dec 2021 04:07:00: end of X-cor INFO @ Thu, 09 Dec 2021 04:07:00: #2 finished! INFO @ Thu, 09 Dec 2021 04:07:00: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:07:00: #2 alternative fragment length(s) may be 4,60,571 bps INFO @ Thu, 09 Dec 2021 04:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.10_model.r WARNING @ Thu, 09 Dec 2021 04:07:00: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:07:00: #2 You may need to consider one of the other alternative d(s): 4,60,571 WARNING @ Thu, 09 Dec 2021 04:07:00: #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 04:07:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:07:01: 4000000 INFO @ Thu, 09 Dec 2021 04:07:07: 5000000 INFO @ Thu, 09 Dec 2021 04:07:13: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:07:14: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:07:18: 7000000 INFO @ Thu, 09 Dec 2021 04:07:22: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:07:22: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:07:22: #1 total tags in treatment: 7605530 INFO @ Thu, 09 Dec 2021 04:07:22: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:07:22: #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 04:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.10_summits.bed INFO @ Thu, 09 Dec 2021 04:07:22: Done! INFO @ Thu, 09 Dec 2021 04:07:22: #1 tags after filtering in treatment: 7605530 INFO @ Thu, 09 Dec 2021 04:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:07:22: #1 finished! INFO @ Thu, 09 Dec 2021 04:07:22: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:07:22: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:07:22: #2 number of paired peaks: 422 WARNING @ Thu, 09 Dec 2021 04:07:22: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Thu, 09 Dec 2021 04:07:22: start model_add_line... INFO @ Thu, 09 Dec 2021 04:07:23: start X-correlation... INFO @ Thu, 09 Dec 2021 04:07:23: end of X-cor INFO @ Thu, 09 Dec 2021 04:07:23: #2 finished! INFO @ Thu, 09 Dec 2021 04:07:23: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:07:23: #2 alternative fragment length(s) may be 4,60,571 bps INFO @ Thu, 09 Dec 2021 04:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.20_model.r WARNING @ Thu, 09 Dec 2021 04:07:23: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:07:23: #2 You may need to consider one of the other alternative d(s): 4,60,571 WARNING @ Thu, 09 Dec 2021 04:07:23: #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 04:07:23: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:07:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:07:38: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569208/SRX10569208.20_summits.bed INFO @ Thu, 09 Dec 2021 04:07:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling