Job ID = 5721086 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,329,820 reads read : 18,659,640 reads written : 18,659,640 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: 01:18:19 9329820 reads; of these: 9329820 (100.00%) were paired; of these: 2626046 (28.15%) aligned concordantly 0 times 1415986 (15.18%) aligned concordantly exactly 1 time 5287788 (56.68%) aligned concordantly >1 times ---- 2626046 pairs aligned concordantly 0 times; of these: 367521 (14.00%) aligned discordantly 1 time ---- 2258525 pairs aligned 0 times concordantly or discordantly; of these: 4517050 mates make up the pairs; of these: 1969575 (43.60%) aligned 0 times 710758 (15.74%) aligned exactly 1 time 1836717 (40.66%) aligned >1 times 89.44% overall alignment rate Time searching: 01:18:19 Overall time: 01:18:19 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 16 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] 2755564 / 6821259 = 0.4040 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 05:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.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 05:58:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:38: 1000000 INFO @ Thu, 16 Apr 2020 05:58:44: 2000000 INFO @ Thu, 16 Apr 2020 05:58:51: 3000000 INFO @ Thu, 16 Apr 2020 05:58:57: 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 @ Thu, 16 Apr 2020 05:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.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 05:59:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:59:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:59:04: 5000000 INFO @ Thu, 16 Apr 2020 05:59:08: 1000000 INFO @ Thu, 16 Apr 2020 05:59:11: 6000000 INFO @ Thu, 16 Apr 2020 05:59:15: 2000000 INFO @ Thu, 16 Apr 2020 05:59:18: 7000000 INFO @ Thu, 16 Apr 2020 05:59:22: 3000000 INFO @ Thu, 16 Apr 2020 05:59:25: 8000000 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 05:59:29: 4000000 INFO @ Thu, 16 Apr 2020 05:59:31: 9000000 INFO @ Thu, 16 Apr 2020 05:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.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 05:59:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:59:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:59:36: 5000000 INFO @ Thu, 16 Apr 2020 05:59:39: 10000000 INFO @ Thu, 16 Apr 2020 05:59:39: 1000000 INFO @ Thu, 16 Apr 2020 05:59:43: 6000000 INFO @ Thu, 16 Apr 2020 05:59:46: 11000000 INFO @ Thu, 16 Apr 2020 05:59:47: 2000000 INFO @ Thu, 16 Apr 2020 05:59:47: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:59:47: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:59:47: #1 total tags in treatment: 3976108 INFO @ Thu, 16 Apr 2020 05:59:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:47: #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 05:59:47: #1 tags after filtering in treatment: 3066655 INFO @ Thu, 16 Apr 2020 05:59:47: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 05:59:47: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:47: #2 number of paired peaks: 6696 INFO @ Thu, 16 Apr 2020 05:59:47: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:47: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:47: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:47: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:47: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 05:59:47: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 05:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.05_model.r WARNING @ Thu, 16 Apr 2020 05:59:47: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:59:47: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Thu, 16 Apr 2020 05:59:47: #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 05:59:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:50: 7000000 INFO @ Thu, 16 Apr 2020 05:59:54: 3000000 INFO @ Thu, 16 Apr 2020 05:59:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:57: 8000000 INFO @ Thu, 16 Apr 2020 05:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.05_summits.bed INFO @ Thu, 16 Apr 2020 05:59:59: Done! INFO @ Thu, 16 Apr 2020 06:00:01: 4000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (10056 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:00:04: 9000000 INFO @ Thu, 16 Apr 2020 06:00:08: 5000000 INFO @ Thu, 16 Apr 2020 06:00:11: 10000000 INFO @ Thu, 16 Apr 2020 06:00:15: 6000000 INFO @ Thu, 16 Apr 2020 06:00:18: 11000000 INFO @ Thu, 16 Apr 2020 06:00:19: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:00:19: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:00:19: #1 total tags in treatment: 3976108 INFO @ Thu, 16 Apr 2020 06:00:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:19: #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 06:00:19: #1 tags after filtering in treatment: 3066655 INFO @ Thu, 16 Apr 2020 06:00:19: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 06:00:19: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:20: #2 number of paired peaks: 6696 INFO @ Thu, 16 Apr 2020 06:00:20: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:20: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:20: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:20: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:20: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 06:00:20: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 06:00:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.10_model.r WARNING @ Thu, 16 Apr 2020 06:00:20: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:00:20: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Thu, 16 Apr 2020 06:00:20: #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 06:00:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:22: 7000000 INFO @ Thu, 16 Apr 2020 06:00:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:00:28: 8000000 INFO @ Thu, 16 Apr 2020 06:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.10_summits.bed INFO @ Thu, 16 Apr 2020 06:00:32: Done! INFO @ Thu, 16 Apr 2020 06:00:35: 9000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6043 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:00:42: 10000000 INFO @ Thu, 16 Apr 2020 06:00:49: 11000000 INFO @ Thu, 16 Apr 2020 06:00:50: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:00:50: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:00:50: #1 total tags in treatment: 3976108 INFO @ Thu, 16 Apr 2020 06:00:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:50: #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 06:00:50: #1 tags after filtering in treatment: 3066655 INFO @ Thu, 16 Apr 2020 06:00:50: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 06:00:50: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:50: #2 number of paired peaks: 6696 INFO @ Thu, 16 Apr 2020 06:00:50: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:50: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:50: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:50: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:50: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 06:00:50: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 06:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.20_model.r WARNING @ Thu, 16 Apr 2020 06:00:50: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:00:50: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Thu, 16 Apr 2020 06:00:50: #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 06:00:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448078/SRX6448078.20_summits.bed INFO @ Thu, 16 Apr 2020 06:01:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2419 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。