Job ID = 6626376 SRX = SRX7262214 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13314924 spots for SRR10581837/SRR10581837.sra Written 13314924 spots for SRR10581837/SRR10581837.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626488 ("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: 00:02:31 13314924 reads; of these: 13314924 (100.00%) were unpaired; of these: 3001752 (22.54%) aligned 0 times 7752864 (58.23%) aligned exactly 1 time 2560308 (19.23%) aligned >1 times 77.46% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 2875356 / 10313172 = 0.2788 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 07:02:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.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 07:02:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:02:40: 1000000 INFO @ Tue, 14 Jul 2020 07:02:46: 2000000 INFO @ Tue, 14 Jul 2020 07:02:52: 3000000 INFO @ Tue, 14 Jul 2020 07:02:57: 4000000 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 07:03:03: 5000000 INFO @ Tue, 14 Jul 2020 07:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.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 07:03:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:03:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:03:10: 6000000 INFO @ Tue, 14 Jul 2020 07:03:12: 1000000 INFO @ Tue, 14 Jul 2020 07:03:16: 7000000 INFO @ Tue, 14 Jul 2020 07:03:19: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:03:19: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:03:19: #1 total tags in treatment: 7437816 INFO @ Tue, 14 Jul 2020 07:03:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:03:19: #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 07:03:19: #1 tags after filtering in treatment: 7437816 INFO @ Tue, 14 Jul 2020 07:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:03:19: #1 finished! INFO @ Tue, 14 Jul 2020 07:03:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:03:20: 2000000 INFO @ Tue, 14 Jul 2020 07:03:20: #2 number of paired peaks: 1092 INFO @ Tue, 14 Jul 2020 07:03:20: start model_add_line... INFO @ Tue, 14 Jul 2020 07:03:20: start X-correlation... INFO @ Tue, 14 Jul 2020 07:03:20: end of X-cor INFO @ Tue, 14 Jul 2020 07:03:20: #2 finished! INFO @ Tue, 14 Jul 2020 07:03:20: #2 predicted fragment length is 74 bps INFO @ Tue, 14 Jul 2020 07:03:20: #2 alternative fragment length(s) may be 3,74,591 bps INFO @ Tue, 14 Jul 2020 07:03:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.05_model.r WARNING @ Tue, 14 Jul 2020 07:03:20: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:03:20: #2 You may need to consider one of the other alternative d(s): 3,74,591 WARNING @ Tue, 14 Jul 2020 07:03:20: #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 07:03:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:03:27: 3000000 BedGraph に変換中... 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 07:03:34: 4000000 INFO @ Tue, 14 Jul 2020 07:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.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 07:03:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:03:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:03:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:03:41: 5000000 INFO @ Tue, 14 Jul 2020 07:03:41: 1000000 INFO @ Tue, 14 Jul 2020 07:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.05_summits.bed INFO @ Tue, 14 Jul 2020 07:03:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (926 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:03:48: 6000000 INFO @ Tue, 14 Jul 2020 07:03:48: 2000000 INFO @ Tue, 14 Jul 2020 07:03:55: 3000000 INFO @ Tue, 14 Jul 2020 07:03:55: 7000000 INFO @ Tue, 14 Jul 2020 07:03:59: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:03:59: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:03:59: #1 total tags in treatment: 7437816 INFO @ Tue, 14 Jul 2020 07:03:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:03:59: #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 07:03:59: #1 tags after filtering in treatment: 7437816 INFO @ Tue, 14 Jul 2020 07:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:03:59: #1 finished! INFO @ Tue, 14 Jul 2020 07:03:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:03:59: #2 number of paired peaks: 1092 INFO @ Tue, 14 Jul 2020 07:03:59: start model_add_line... INFO @ Tue, 14 Jul 2020 07:03:59: start X-correlation... INFO @ Tue, 14 Jul 2020 07:03:59: end of X-cor INFO @ Tue, 14 Jul 2020 07:03:59: #2 finished! INFO @ Tue, 14 Jul 2020 07:03:59: #2 predicted fragment length is 74 bps INFO @ Tue, 14 Jul 2020 07:03:59: #2 alternative fragment length(s) may be 3,74,591 bps INFO @ Tue, 14 Jul 2020 07:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.10_model.r WARNING @ Tue, 14 Jul 2020 07:03:59: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:03:59: #2 You may need to consider one of the other alternative d(s): 3,74,591 WARNING @ Tue, 14 Jul 2020 07:03:59: #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 07:03:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:04:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:04:08: 5000000 INFO @ Tue, 14 Jul 2020 07:04:14: 6000000 INFO @ Tue, 14 Jul 2020 07:04:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:04:21: 7000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:04:23: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:04:23: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:04:23: #1 total tags in treatment: 7437816 INFO @ Tue, 14 Jul 2020 07:04:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:04:23: #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 07:04:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:04:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:04:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.10_summits.bed INFO @ Tue, 14 Jul 2020 07:04:23: #1 tags after filtering in treatment: 7437816 INFO @ Tue, 14 Jul 2020 07:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:04:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:04:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:04:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:04:24: #2 number of paired peaks: 1092 INFO @ Tue, 14 Jul 2020 07:04:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:04:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:04:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:04:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:04:24: #2 predicted fragment length is 74 bps INFO @ Tue, 14 Jul 2020 07:04:24: #2 alternative fragment length(s) may be 3,74,591 bps INFO @ Tue, 14 Jul 2020 07:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.20_model.r WARNING @ Tue, 14 Jul 2020 07:04:24: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:04:24: #2 You may need to consider one of the other alternative d(s): 3,74,591 WARNING @ Tue, 14 Jul 2020 07:04:24: #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 07:04:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:04:39: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:04:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262214/SRX7262214.20_summits.bed INFO @ Tue, 14 Jul 2020 07:04:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (196 records, 4 fields): 16 millis CompletedMACS2peakCalling