Job ID = 5721124 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,515,478 reads read : 13,030,956 reads written : 13,030,956 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: 00:18:47 6515478 reads; of these: 6515478 (100.00%) were paired; of these: 798562 (12.26%) aligned concordantly 0 times 3910548 (60.02%) aligned concordantly exactly 1 time 1806368 (27.72%) aligned concordantly >1 times ---- 798562 pairs aligned concordantly 0 times; of these: 258405 (32.36%) aligned discordantly 1 time ---- 540157 pairs aligned 0 times concordantly or discordantly; of these: 1080314 mates make up the pairs; of these: 663490 (61.42%) aligned 0 times 177228 (16.41%) aligned exactly 1 time 239596 (22.18%) aligned >1 times 94.91% overall alignment rate Time searching: 00:18:47 Overall time: 00:18:47 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] 340275 / 5917205 = 0.0575 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 05:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.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 05:24:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:24:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:25:04: 1000000 INFO @ Thu, 16 Apr 2020 05:25:12: 2000000 INFO @ Thu, 16 Apr 2020 05:25:19: 3000000 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 05:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.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 05:25:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:25:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:25:27: 4000000 INFO @ Thu, 16 Apr 2020 05:25:33: 1000000 INFO @ Thu, 16 Apr 2020 05:25:35: 5000000 INFO @ Thu, 16 Apr 2020 05:25:41: 2000000 INFO @ Thu, 16 Apr 2020 05:25:43: 6000000 INFO @ Thu, 16 Apr 2020 05:25:50: 3000000 INFO @ Thu, 16 Apr 2020 05:25:52: 7000000 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 05:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.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 05:25:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:25:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:25:58: 4000000 INFO @ Thu, 16 Apr 2020 05:26:00: 8000000 INFO @ Thu, 16 Apr 2020 05:26:03: 1000000 INFO @ Thu, 16 Apr 2020 05:26:06: 5000000 INFO @ Thu, 16 Apr 2020 05:26:08: 9000000 INFO @ Thu, 16 Apr 2020 05:26:11: 2000000 INFO @ Thu, 16 Apr 2020 05:26:15: 6000000 INFO @ Thu, 16 Apr 2020 05:26:16: 10000000 INFO @ Thu, 16 Apr 2020 05:26:20: 3000000 INFO @ Thu, 16 Apr 2020 05:26:23: 7000000 INFO @ Thu, 16 Apr 2020 05:26:25: 11000000 INFO @ Thu, 16 Apr 2020 05:26:28: 4000000 INFO @ Thu, 16 Apr 2020 05:26:31: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:26:31: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:26:31: #1 total tags in treatment: 5382331 INFO @ Thu, 16 Apr 2020 05:26:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:26:31: #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 05:26:31: #1 tags after filtering in treatment: 5182040 INFO @ Thu, 16 Apr 2020 05:26:31: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:26:31: #1 finished! INFO @ Thu, 16 Apr 2020 05:26:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:26:31: #2 number of paired peaks: 1072 INFO @ Thu, 16 Apr 2020 05:26:31: start model_add_line... INFO @ Thu, 16 Apr 2020 05:26:31: start X-correlation... INFO @ Thu, 16 Apr 2020 05:26:31: end of X-cor INFO @ Thu, 16 Apr 2020 05:26:31: #2 finished! INFO @ Thu, 16 Apr 2020 05:26:31: #2 predicted fragment length is 132 bps INFO @ Thu, 16 Apr 2020 05:26:31: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 16 Apr 2020 05:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.05_model.r WARNING @ Thu, 16 Apr 2020 05:26:31: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:26:31: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 16 Apr 2020 05:26:31: #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 05:26:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:26:32: 8000000 INFO @ Thu, 16 Apr 2020 05:26:36: 5000000 INFO @ Thu, 16 Apr 2020 05:26:39: 9000000 INFO @ Thu, 16 Apr 2020 05:26:44: 6000000 INFO @ Thu, 16 Apr 2020 05:26:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:26:47: 10000000 INFO @ Thu, 16 Apr 2020 05:26:51: 7000000 INFO @ Thu, 16 Apr 2020 05:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.05_summits.bed INFO @ Thu, 16 Apr 2020 05:26:52: Done! INFO @ Thu, 16 Apr 2020 05:26:55: 11000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1547 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:26:59: 8000000 INFO @ Thu, 16 Apr 2020 05:27:00: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:27:00: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:27:00: #1 total tags in treatment: 5382331 INFO @ Thu, 16 Apr 2020 05:27:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:27:00: #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 05:27:00: #1 tags after filtering in treatment: 5182040 INFO @ Thu, 16 Apr 2020 05:27:00: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:27:00: #1 finished! INFO @ Thu, 16 Apr 2020 05:27:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:27:00: #2 number of paired peaks: 1072 INFO @ Thu, 16 Apr 2020 05:27:00: start model_add_line... INFO @ Thu, 16 Apr 2020 05:27:00: start X-correlation... INFO @ Thu, 16 Apr 2020 05:27:00: end of X-cor INFO @ Thu, 16 Apr 2020 05:27:00: #2 finished! INFO @ Thu, 16 Apr 2020 05:27:00: #2 predicted fragment length is 132 bps INFO @ Thu, 16 Apr 2020 05:27:00: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 16 Apr 2020 05:27:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.10_model.r WARNING @ Thu, 16 Apr 2020 05:27:00: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:27:00: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 16 Apr 2020 05:27:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:27:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:27:06: 9000000 INFO @ Thu, 16 Apr 2020 05:27:14: 10000000 INFO @ Thu, 16 Apr 2020 05:27:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:27:21: 11000000 INFO @ Thu, 16 Apr 2020 05:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.10_summits.bed INFO @ Thu, 16 Apr 2020 05:27:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (973 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:27:26: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:27:26: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:27:26: #1 total tags in treatment: 5382331 INFO @ Thu, 16 Apr 2020 05:27:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:27:26: #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 05:27:26: #1 tags after filtering in treatment: 5182040 INFO @ Thu, 16 Apr 2020 05:27:26: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:27:26: #1 finished! INFO @ Thu, 16 Apr 2020 05:27:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:27:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:27:26: #2 number of paired peaks: 1072 INFO @ Thu, 16 Apr 2020 05:27:26: start model_add_line... INFO @ Thu, 16 Apr 2020 05:27:27: start X-correlation... INFO @ Thu, 16 Apr 2020 05:27:27: end of X-cor INFO @ Thu, 16 Apr 2020 05:27:27: #2 finished! INFO @ Thu, 16 Apr 2020 05:27:27: #2 predicted fragment length is 132 bps INFO @ Thu, 16 Apr 2020 05:27:27: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 16 Apr 2020 05:27:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.20_model.r WARNING @ Thu, 16 Apr 2020 05:27:27: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:27:27: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 16 Apr 2020 05:27:27: #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 05:27:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:27:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:27:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708266/SRX6708266.20_summits.bed INFO @ Thu, 16 Apr 2020 05:27:46: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。