Job ID = 12264743 SRX = SRX2332996 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36024207 spots for SRR5000676/SRR5000676.sra Written 36024207 spots for SRR5000676/SRR5000676.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265219 ("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: 00:12:57 36024207 reads; of these: 36024207 (100.00%) were paired; of these: 33073692 (91.81%) aligned concordantly 0 times 2174725 (6.04%) aligned concordantly exactly 1 time 775790 (2.15%) aligned concordantly >1 times ---- 33073692 pairs aligned concordantly 0 times; of these: 567387 (1.72%) aligned discordantly 1 time ---- 32506305 pairs aligned 0 times concordantly or discordantly; of these: 65012610 mates make up the pairs; of these: 64569556 (99.32%) aligned 0 times 121694 (0.19%) aligned exactly 1 time 321360 (0.49%) aligned >1 times 10.38% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 988075 / 3497165 = 0.2825 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.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 @ Sat, 03 Apr 2021 06:12:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:12:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:12:08: 1000000 INFO @ Sat, 03 Apr 2021 06:12:15: 2000000 INFO @ Sat, 03 Apr 2021 06:12:22: 3000000 INFO @ Sat, 03 Apr 2021 06:12:29: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.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 @ Sat, 03 Apr 2021 06:12:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:12:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:12:36: 5000000 INFO @ Sat, 03 Apr 2021 06:12:39: 1000000 INFO @ Sat, 03 Apr 2021 06:12:40: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:12:40: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:12:40: #1 total tags in treatment: 2072555 INFO @ Sat, 03 Apr 2021 06:12:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:12:40: #1 tags after filtering in treatment: 1591476 INFO @ Sat, 03 Apr 2021 06:12:40: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:12:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:40: #2 number of paired peaks: 1142 INFO @ Sat, 03 Apr 2021 06:12:40: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:40: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:40: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:40: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:40: #2 predicted fragment length is 160 bps INFO @ Sat, 03 Apr 2021 06:12:40: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 03 Apr 2021 06:12:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.05_model.r WARNING @ Sat, 03 Apr 2021 06:12:40: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:40: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 03 Apr 2021 06:12:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:12:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:46: 2000000 INFO @ Sat, 03 Apr 2021 06:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.05_summits.bed INFO @ Sat, 03 Apr 2021 06:12:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1324 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:12:53: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:13:00: 4000000 INFO @ Sat, 03 Apr 2021 06:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.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 @ Sat, 03 Apr 2021 06:13:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:13:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:13:08: 5000000 INFO @ Sat, 03 Apr 2021 06:13:09: 1000000 INFO @ Sat, 03 Apr 2021 06:13:12: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:13:12: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:13:12: #1 total tags in treatment: 2072555 INFO @ Sat, 03 Apr 2021 06:13:12: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:13:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:13:12: #1 tags after filtering in treatment: 1591476 INFO @ Sat, 03 Apr 2021 06:13:12: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:13:12: #1 finished! INFO @ Sat, 03 Apr 2021 06:13:12: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:13:12: #2 number of paired peaks: 1142 INFO @ Sat, 03 Apr 2021 06:13:12: start model_add_line... INFO @ Sat, 03 Apr 2021 06:13:12: start X-correlation... INFO @ Sat, 03 Apr 2021 06:13:12: end of X-cor INFO @ Sat, 03 Apr 2021 06:13:12: #2 finished! INFO @ Sat, 03 Apr 2021 06:13:12: #2 predicted fragment length is 160 bps INFO @ Sat, 03 Apr 2021 06:13:12: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 03 Apr 2021 06:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.10_model.r WARNING @ Sat, 03 Apr 2021 06:13:12: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:13:12: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 03 Apr 2021 06:13:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:13:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:13:16: 2000000 INFO @ Sat, 03 Apr 2021 06:13:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:13:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.10_summits.bed INFO @ Sat, 03 Apr 2021 06:13:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:13:23: 3000000 INFO @ Sat, 03 Apr 2021 06:13:30: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:13:37: 5000000 INFO @ Sat, 03 Apr 2021 06:13:40: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:13:40: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:13:40: #1 total tags in treatment: 2072555 INFO @ Sat, 03 Apr 2021 06:13:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:13:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:13:40: #1 tags after filtering in treatment: 1591476 INFO @ Sat, 03 Apr 2021 06:13:40: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:13:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:13:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:13:40: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:13:41: #2 number of paired peaks: 1142 INFO @ Sat, 03 Apr 2021 06:13:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:13:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:13:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:13:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:13:41: #2 predicted fragment length is 160 bps INFO @ Sat, 03 Apr 2021 06:13:41: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 03 Apr 2021 06:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.20_model.r WARNING @ Sat, 03 Apr 2021 06:13:41: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:13:41: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 03 Apr 2021 06:13:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:13:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:13:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:13:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332996/SRX2332996.20_summits.bed INFO @ Sat, 03 Apr 2021 06:13:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis CompletedMACS2peakCalling