Job ID = 5721077 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,108,451 reads read : 30,216,902 reads written : 30,216,902 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: 01:46:29 15108451 reads; of these: 15108451 (100.00%) were paired; of these: 3540740 (23.44%) aligned concordantly 0 times 2701826 (17.88%) aligned concordantly exactly 1 time 8865885 (58.68%) aligned concordantly >1 times ---- 3540740 pairs aligned concordantly 0 times; of these: 492897 (13.92%) aligned discordantly 1 time ---- 3047843 pairs aligned 0 times concordantly or discordantly; of these: 6095686 mates make up the pairs; of these: 3072226 (50.40%) aligned 0 times 1096930 (18.00%) aligned exactly 1 time 1926530 (31.60%) aligned >1 times 89.83% overall alignment rate Time searching: 01:46:30 Overall time: 01:46:30 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 20 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] 6408613 / 11560401 = 0.5544 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 06:30:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.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 06:30:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:30:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:30:57: 1000000 INFO @ Thu, 16 Apr 2020 06:31:05: 2000000 INFO @ Thu, 16 Apr 2020 06:31:13: 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 06:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.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 06:31:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:31:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:31:21: 4000000 INFO @ Thu, 16 Apr 2020 06:31:26: 1000000 INFO @ Thu, 16 Apr 2020 06:31:29: 5000000 INFO @ Thu, 16 Apr 2020 06:31:32: 2000000 INFO @ Thu, 16 Apr 2020 06:31:37: 6000000 INFO @ Thu, 16 Apr 2020 06:31:39: 3000000 INFO @ Thu, 16 Apr 2020 06:31:45: 7000000 INFO @ Thu, 16 Apr 2020 06:31:45: 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 06:31:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.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 06:31:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:31:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:31:52: 5000000 INFO @ Thu, 16 Apr 2020 06:31:53: 8000000 INFO @ Thu, 16 Apr 2020 06:31:57: 1000000 INFO @ Thu, 16 Apr 2020 06:31:58: 6000000 INFO @ Thu, 16 Apr 2020 06:32:01: 9000000 INFO @ Thu, 16 Apr 2020 06:32:04: 7000000 INFO @ Thu, 16 Apr 2020 06:32:05: 2000000 INFO @ Thu, 16 Apr 2020 06:32:09: 10000000 INFO @ Thu, 16 Apr 2020 06:32:11: 8000000 INFO @ Thu, 16 Apr 2020 06:32:13: 3000000 INFO @ Thu, 16 Apr 2020 06:32:17: 11000000 INFO @ Thu, 16 Apr 2020 06:32:17: 9000000 INFO @ Thu, 16 Apr 2020 06:32:21: 4000000 INFO @ Thu, 16 Apr 2020 06:32:24: 10000000 INFO @ Thu, 16 Apr 2020 06:32:25: 12000000 INFO @ Thu, 16 Apr 2020 06:32:29: 5000000 INFO @ Thu, 16 Apr 2020 06:32:30: 11000000 INFO @ Thu, 16 Apr 2020 06:32:33: 13000000 INFO @ Thu, 16 Apr 2020 06:32:36: 12000000 INFO @ Thu, 16 Apr 2020 06:32:38: 6000000 INFO @ Thu, 16 Apr 2020 06:32:41: 14000000 INFO @ Thu, 16 Apr 2020 06:32:43: 13000000 INFO @ Thu, 16 Apr 2020 06:32:44: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:32:44: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:32:44: #1 total tags in treatment: 5229422 INFO @ Thu, 16 Apr 2020 06:32:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:32:44: #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 06:32:44: #1 tags after filtering in treatment: 3989118 INFO @ Thu, 16 Apr 2020 06:32:44: #1 Redundant rate of treatment: 0.24 INFO @ Thu, 16 Apr 2020 06:32:44: #1 finished! INFO @ Thu, 16 Apr 2020 06:32:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:32:45: #2 number of paired peaks: 6818 INFO @ Thu, 16 Apr 2020 06:32:45: start model_add_line... INFO @ Thu, 16 Apr 2020 06:32:45: start X-correlation... INFO @ Thu, 16 Apr 2020 06:32:45: end of X-cor INFO @ Thu, 16 Apr 2020 06:32:45: #2 finished! INFO @ Thu, 16 Apr 2020 06:32:45: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 06:32:45: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 06:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.05_model.r WARNING @ Thu, 16 Apr 2020 06:32:45: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:32:45: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Thu, 16 Apr 2020 06:32:45: #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 06:32:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:32:46: 7000000 INFO @ Thu, 16 Apr 2020 06:32:49: 14000000 INFO @ Thu, 16 Apr 2020 06:32:51: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:32:51: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:32:51: #1 total tags in treatment: 5229422 INFO @ Thu, 16 Apr 2020 06:32:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:32:51: #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 06:32:51: #1 tags after filtering in treatment: 3989118 INFO @ Thu, 16 Apr 2020 06:32:51: #1 Redundant rate of treatment: 0.24 INFO @ Thu, 16 Apr 2020 06:32:51: #1 finished! INFO @ Thu, 16 Apr 2020 06:32:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:32:52: #2 number of paired peaks: 6818 INFO @ Thu, 16 Apr 2020 06:32:52: start model_add_line... INFO @ Thu, 16 Apr 2020 06:32:52: start X-correlation... INFO @ Thu, 16 Apr 2020 06:32:52: end of X-cor INFO @ Thu, 16 Apr 2020 06:32:52: #2 finished! INFO @ Thu, 16 Apr 2020 06:32:52: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 06:32:52: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 06:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.10_model.r WARNING @ Thu, 16 Apr 2020 06:32:52: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:32:52: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Thu, 16 Apr 2020 06:32:52: #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 06:32:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:32:53: 8000000 INFO @ Thu, 16 Apr 2020 06:32:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:33:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:33:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.05_summits.bed INFO @ Thu, 16 Apr 2020 06:33:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (11293 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:33:01: 9000000 INFO @ Thu, 16 Apr 2020 06:33:02: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.10_summits.bed INFO @ Thu, 16 Apr 2020 06:33:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8454 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:33:09: 10000000 INFO @ Thu, 16 Apr 2020 06:33:17: 11000000 INFO @ Thu, 16 Apr 2020 06:33:25: 12000000 INFO @ Thu, 16 Apr 2020 06:33:32: 13000000 INFO @ Thu, 16 Apr 2020 06:33:40: 14000000 INFO @ Thu, 16 Apr 2020 06:33:43: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 06:33:43: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 06:33:43: #1 total tags in treatment: 5229422 INFO @ Thu, 16 Apr 2020 06:33:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:33:43: #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 06:33:43: #1 tags after filtering in treatment: 3989118 INFO @ Thu, 16 Apr 2020 06:33:43: #1 Redundant rate of treatment: 0.24 INFO @ Thu, 16 Apr 2020 06:33:43: #1 finished! INFO @ Thu, 16 Apr 2020 06:33:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:33:43: #2 number of paired peaks: 6818 INFO @ Thu, 16 Apr 2020 06:33:43: start model_add_line... INFO @ Thu, 16 Apr 2020 06:33:43: start X-correlation... INFO @ Thu, 16 Apr 2020 06:33:43: end of X-cor INFO @ Thu, 16 Apr 2020 06:33:43: #2 finished! INFO @ Thu, 16 Apr 2020 06:33:43: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 06:33:43: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 06:33:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.20_model.r WARNING @ Thu, 16 Apr 2020 06:33:43: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:33:43: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Thu, 16 Apr 2020 06:33:43: #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 06:33:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:33:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:33:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448073/SRX6448073.20_summits.bed INFO @ Thu, 16 Apr 2020 06:33:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4765 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。