Job ID = 5721127 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,214,342 reads read : 10,428,684 reads written : 10,428,684 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:10 5214342 reads; of these: 5214342 (100.00%) were paired; of these: 539754 (10.35%) aligned concordantly 0 times 3297519 (63.24%) aligned concordantly exactly 1 time 1377069 (26.41%) aligned concordantly >1 times ---- 539754 pairs aligned concordantly 0 times; of these: 181446 (33.62%) aligned discordantly 1 time ---- 358308 pairs aligned 0 times concordantly or discordantly; of these: 716616 mates make up the pairs; of these: 392290 (54.74%) aligned 0 times 151708 (21.17%) aligned exactly 1 time 172618 (24.09%) aligned >1 times 96.24% overall alignment rate Time searching: 00:12:10 Overall time: 00:12:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 266687 / 4825883 = 0.0553 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 @ Thu, 16 Apr 2020 05:22:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 05:22:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:22:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:22:42: 1000000 INFO @ Thu, 16 Apr 2020 05:22:47: 2000000 INFO @ Thu, 16 Apr 2020 05:22:52: 3000000 INFO @ Thu, 16 Apr 2020 05:22:57: 4000000 INFO @ Thu, 16 Apr 2020 05:23:02: 5000000 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 @ Thu, 16 Apr 2020 05:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 05:23:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:23:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:23:07: 6000000 INFO @ Thu, 16 Apr 2020 05:23:11: 1000000 INFO @ Thu, 16 Apr 2020 05:23:12: 7000000 INFO @ Thu, 16 Apr 2020 05:23:17: 2000000 INFO @ Thu, 16 Apr 2020 05:23:18: 8000000 INFO @ Thu, 16 Apr 2020 05:23:22: 3000000 INFO @ Thu, 16 Apr 2020 05:23:23: 9000000 INFO @ Thu, 16 Apr 2020 05:23:26: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:23:26: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:23:26: #1 total tags in treatment: 4412007 INFO @ Thu, 16 Apr 2020 05:23:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:23:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:23:26: #1 tags after filtering in treatment: 4247823 INFO @ Thu, 16 Apr 2020 05:23:26: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:23:26: #1 finished! INFO @ Thu, 16 Apr 2020 05:23:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:23:26: #2 number of paired peaks: 1353 INFO @ Thu, 16 Apr 2020 05:23:26: start model_add_line... INFO @ Thu, 16 Apr 2020 05:23:26: start X-correlation... INFO @ Thu, 16 Apr 2020 05:23:26: end of X-cor INFO @ Thu, 16 Apr 2020 05:23:26: #2 finished! INFO @ Thu, 16 Apr 2020 05:23:26: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 05:23:26: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 16 Apr 2020 05:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.05_model.r WARNING @ Thu, 16 Apr 2020 05:23:26: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:23:26: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Thu, 16 Apr 2020 05:23:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:23:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:23:28: 4000000 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 @ Thu, 16 Apr 2020 05:23:33: 5000000 INFO @ Thu, 16 Apr 2020 05:23:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 05:23:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:23:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:23:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:23:38: 6000000 INFO @ Thu, 16 Apr 2020 05:23:40: 1000000 INFO @ Thu, 16 Apr 2020 05:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.05_summits.bed INFO @ Thu, 16 Apr 2020 05:23:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1340 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:23:43: 7000000 INFO @ Thu, 16 Apr 2020 05:23:45: 2000000 INFO @ Thu, 16 Apr 2020 05:23:49: 8000000 INFO @ Thu, 16 Apr 2020 05:23:51: 3000000 INFO @ Thu, 16 Apr 2020 05:23:54: 9000000 INFO @ Thu, 16 Apr 2020 05:23:56: 4000000 INFO @ Thu, 16 Apr 2020 05:23:56: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:23:56: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:23:56: #1 total tags in treatment: 4412007 INFO @ Thu, 16 Apr 2020 05:23:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:23:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:23:57: #1 tags after filtering in treatment: 4247823 INFO @ Thu, 16 Apr 2020 05:23:57: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:23:57: #1 finished! INFO @ Thu, 16 Apr 2020 05:23:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:23:57: #2 number of paired peaks: 1353 INFO @ Thu, 16 Apr 2020 05:23:57: start model_add_line... INFO @ Thu, 16 Apr 2020 05:23:57: start X-correlation... INFO @ Thu, 16 Apr 2020 05:23:57: end of X-cor INFO @ Thu, 16 Apr 2020 05:23:57: #2 finished! INFO @ Thu, 16 Apr 2020 05:23:57: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 05:23:57: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 16 Apr 2020 05:23:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.10_model.r WARNING @ Thu, 16 Apr 2020 05:23:57: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:23:57: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Thu, 16 Apr 2020 05:23:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:23:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:23:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:24:01: 5000000 INFO @ Thu, 16 Apr 2020 05:24:06: 6000000 INFO @ Thu, 16 Apr 2020 05:24:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.10_summits.bed INFO @ Thu, 16 Apr 2020 05:24:11: Done! INFO @ Thu, 16 Apr 2020 05:24:11: 7000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (795 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:24:16: 8000000 INFO @ Thu, 16 Apr 2020 05:24:21: 9000000 INFO @ Thu, 16 Apr 2020 05:24:24: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:24:24: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:24:24: #1 total tags in treatment: 4412007 INFO @ Thu, 16 Apr 2020 05:24:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:24:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:24:24: #1 tags after filtering in treatment: 4247823 INFO @ Thu, 16 Apr 2020 05:24:24: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:24:24: #1 finished! INFO @ Thu, 16 Apr 2020 05:24:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:24:24: #2 number of paired peaks: 1353 INFO @ Thu, 16 Apr 2020 05:24:24: start model_add_line... INFO @ Thu, 16 Apr 2020 05:24:24: start X-correlation... INFO @ Thu, 16 Apr 2020 05:24:24: end of X-cor INFO @ Thu, 16 Apr 2020 05:24:24: #2 finished! INFO @ Thu, 16 Apr 2020 05:24:24: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 05:24:24: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 16 Apr 2020 05:24:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.20_model.r WARNING @ Thu, 16 Apr 2020 05:24:24: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:24:24: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Thu, 16 Apr 2020 05:24:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:24:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:24:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:24:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708269/SRX6708269.20_summits.bed INFO @ Thu, 16 Apr 2020 05:24:38: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (344 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。