Job ID = 6626421 SRX = SRX7630544 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31475414 spots for SRR10964906/SRR10964906.sra Written 31475414 spots for SRR10964906/SRR10964906.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626577 ("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: 00:02:26 31475414 reads; of these: 31475414 (100.00%) were unpaired; of these: 26402266 (83.88%) aligned 0 times 4285611 (13.62%) aligned exactly 1 time 787537 (2.50%) aligned >1 times 16.12% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1955193 / 5073148 = 0.3854 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.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 @ Tue, 14 Jul 2020 07:05:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:05:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:05:46: 1000000 INFO @ Tue, 14 Jul 2020 07:05:52: 2000000 INFO @ Tue, 14 Jul 2020 07:05:59: 3000000 INFO @ Tue, 14 Jul 2020 07:05:59: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:05:59: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:05:59: #1 total tags in treatment: 3117955 INFO @ Tue, 14 Jul 2020 07:05:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:05:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:05:59: #1 tags after filtering in treatment: 3117955 INFO @ Tue, 14 Jul 2020 07:05:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:05:59: #1 finished! INFO @ Tue, 14 Jul 2020 07:05:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:05:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:06:00: #2 number of paired peaks: 684 WARNING @ Tue, 14 Jul 2020 07:06:00: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 14 Jul 2020 07:06:00: start model_add_line... INFO @ Tue, 14 Jul 2020 07:06:00: start X-correlation... INFO @ Tue, 14 Jul 2020 07:06:00: end of X-cor INFO @ Tue, 14 Jul 2020 07:06:00: #2 finished! INFO @ Tue, 14 Jul 2020 07:06:00: #2 predicted fragment length is 82 bps INFO @ Tue, 14 Jul 2020 07:06:00: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 14 Jul 2020 07:06:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.05_model.r WARNING @ Tue, 14 Jul 2020 07:06:00: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:06:00: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 14 Jul 2020 07:06:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:06:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:06:07: #3 Call peaks for each chromosome... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.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 @ Tue, 14 Jul 2020 07:06:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:06:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:06:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.05_summits.bed INFO @ Tue, 14 Jul 2020 07:06:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (492 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:06:14: 1000000 INFO @ Tue, 14 Jul 2020 07:06:20: 2000000 INFO @ Tue, 14 Jul 2020 07:06:26: 3000000 INFO @ Tue, 14 Jul 2020 07:06:26: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:06:26: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:06:26: #1 total tags in treatment: 3117955 INFO @ Tue, 14 Jul 2020 07:06:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:06:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:06:26: #1 tags after filtering in treatment: 3117955 INFO @ Tue, 14 Jul 2020 07:06:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:06:26: #1 finished! INFO @ Tue, 14 Jul 2020 07:06:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:06:26: #2 number of paired peaks: 684 WARNING @ Tue, 14 Jul 2020 07:06:26: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 14 Jul 2020 07:06:26: start model_add_line... INFO @ Tue, 14 Jul 2020 07:06:26: start X-correlation... INFO @ Tue, 14 Jul 2020 07:06:26: end of X-cor INFO @ Tue, 14 Jul 2020 07:06:26: #2 finished! INFO @ Tue, 14 Jul 2020 07:06:26: #2 predicted fragment length is 82 bps INFO @ Tue, 14 Jul 2020 07:06:26: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 14 Jul 2020 07:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.10_model.r WARNING @ Tue, 14 Jul 2020 07:06:26: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:06:26: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 14 Jul 2020 07:06:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:06:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:06:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.10_peaks.narrowPeak BedGraph に変換中... INFO @ Tue, 14 Jul 2020 07:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.10_summits.bed INFO @ Tue, 14 Jul 2020 07:06:37: Done! WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (319 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.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 @ Tue, 14 Jul 2020 07:06:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:46: 1000000 INFO @ Tue, 14 Jul 2020 07:06:52: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:06:59: 3000000 INFO @ Tue, 14 Jul 2020 07:06:59: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:06:59: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:06:59: #1 total tags in treatment: 3117955 INFO @ Tue, 14 Jul 2020 07:06:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:06:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:06:59: #1 tags after filtering in treatment: 3117955 INFO @ Tue, 14 Jul 2020 07:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:06:59: #1 finished! INFO @ Tue, 14 Jul 2020 07:06:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:00: #2 number of paired peaks: 684 WARNING @ Tue, 14 Jul 2020 07:07:00: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:00: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:00: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:00: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:00: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:00: #2 predicted fragment length is 82 bps INFO @ Tue, 14 Jul 2020 07:07:00: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 14 Jul 2020 07:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.20_model.r WARNING @ Tue, 14 Jul 2020 07:07:00: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:07:00: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 14 Jul 2020 07:07:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:07:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630544/SRX7630544.20_summits.bed INFO @ Tue, 14 Jul 2020 07:07:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 14 millis CompletedMACS2peakCalling