Job ID = 6626574 SRX = SRX7224576 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13066890 spots for SRR10541128/SRR10541128.sra Written 13066890 spots for SRR10541128/SRR10541128.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626786 ("srTdm6") 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: 00:38:01 13066890 reads; of these: 13066890 (100.00%) were paired; of these: 3736847 (28.60%) aligned concordantly 0 times 7407034 (56.69%) aligned concordantly exactly 1 time 1923009 (14.72%) aligned concordantly >1 times ---- 3736847 pairs aligned concordantly 0 times; of these: 2121935 (56.78%) aligned discordantly 1 time ---- 1614912 pairs aligned 0 times concordantly or discordantly; of these: 3229824 mates make up the pairs; of these: 1956534 (60.58%) aligned 0 times 308025 (9.54%) aligned exactly 1 time 965265 (29.89%) aligned >1 times 92.51% overall alignment rate Time searching: 00:38:01 Overall time: 00:38:01 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] 1547885 / 11256169 = 0.1375 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 @ Tue, 14 Jul 2020 08:25:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.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 @ Tue, 14 Jul 2020 08:25:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:25:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:25:35: 1000000 INFO @ Tue, 14 Jul 2020 08:25:43: 2000000 INFO @ Tue, 14 Jul 2020 08:25:50: 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 @ Tue, 14 Jul 2020 08:25:57: 4000000 INFO @ Tue, 14 Jul 2020 08:25:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.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 @ Tue, 14 Jul 2020 08:25:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:25:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:26:05: 5000000 INFO @ Tue, 14 Jul 2020 08:26:07: 1000000 INFO @ Tue, 14 Jul 2020 08:26:14: 6000000 INFO @ Tue, 14 Jul 2020 08:26:15: 2000000 INFO @ Tue, 14 Jul 2020 08:26:22: 7000000 INFO @ Tue, 14 Jul 2020 08:26:23: 3000000 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 @ Tue, 14 Jul 2020 08:26:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.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 @ Tue, 14 Jul 2020 08:26:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:26:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:26:30: 8000000 INFO @ Tue, 14 Jul 2020 08:26:31: 4000000 INFO @ Tue, 14 Jul 2020 08:26:39: 9000000 INFO @ Tue, 14 Jul 2020 08:26:39: 1000000 INFO @ Tue, 14 Jul 2020 08:26:40: 5000000 INFO @ Tue, 14 Jul 2020 08:26:47: 10000000 INFO @ Tue, 14 Jul 2020 08:26:48: 6000000 INFO @ Tue, 14 Jul 2020 08:26:49: 2000000 INFO @ Tue, 14 Jul 2020 08:26:56: 11000000 INFO @ Tue, 14 Jul 2020 08:26:56: 7000000 INFO @ Tue, 14 Jul 2020 08:26:59: 3000000 INFO @ Tue, 14 Jul 2020 08:27:04: 12000000 INFO @ Tue, 14 Jul 2020 08:27:05: 8000000 INFO @ Tue, 14 Jul 2020 08:27:09: 4000000 INFO @ Tue, 14 Jul 2020 08:27:13: 13000000 INFO @ Tue, 14 Jul 2020 08:27:13: 9000000 INFO @ Tue, 14 Jul 2020 08:27:19: 5000000 INFO @ Tue, 14 Jul 2020 08:27:21: 14000000 INFO @ Tue, 14 Jul 2020 08:27:22: 10000000 INFO @ Tue, 14 Jul 2020 08:27:29: 6000000 INFO @ Tue, 14 Jul 2020 08:27:29: 15000000 INFO @ Tue, 14 Jul 2020 08:27:30: 11000000 INFO @ Tue, 14 Jul 2020 08:27:38: 16000000 INFO @ Tue, 14 Jul 2020 08:27:38: 12000000 INFO @ Tue, 14 Jul 2020 08:27:40: 7000000 INFO @ Tue, 14 Jul 2020 08:27:46: 17000000 INFO @ Tue, 14 Jul 2020 08:27:47: 13000000 INFO @ Tue, 14 Jul 2020 08:27:50: 8000000 INFO @ Tue, 14 Jul 2020 08:27:55: 18000000 INFO @ Tue, 14 Jul 2020 08:27:55: 14000000 INFO @ Tue, 14 Jul 2020 08:28:01: 9000000 INFO @ Tue, 14 Jul 2020 08:28:03: 15000000 INFO @ Tue, 14 Jul 2020 08:28:03: 19000000 INFO @ Tue, 14 Jul 2020 08:28:12: 16000000 INFO @ Tue, 14 Jul 2020 08:28:12: 20000000 INFO @ Tue, 14 Jul 2020 08:28:12: 10000000 INFO @ Tue, 14 Jul 2020 08:28:20: 17000000 INFO @ Tue, 14 Jul 2020 08:28:20: 21000000 INFO @ Tue, 14 Jul 2020 08:28:21: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:28:21: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:28:21: #1 total tags in treatment: 8012718 INFO @ Tue, 14 Jul 2020 08:28:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:28:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:28:21: #1 tags after filtering in treatment: 7626302 INFO @ Tue, 14 Jul 2020 08:28:21: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 08:28:21: #1 finished! INFO @ Tue, 14 Jul 2020 08:28:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:28:21: #2 number of paired peaks: 244 WARNING @ Tue, 14 Jul 2020 08:28:21: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 14 Jul 2020 08:28:21: start model_add_line... INFO @ Tue, 14 Jul 2020 08:28:22: start X-correlation... INFO @ Tue, 14 Jul 2020 08:28:22: end of X-cor INFO @ Tue, 14 Jul 2020 08:28:22: #2 finished! INFO @ Tue, 14 Jul 2020 08:28:22: #2 predicted fragment length is 183 bps INFO @ Tue, 14 Jul 2020 08:28:22: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 14 Jul 2020 08:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.05_model.r WARNING @ Tue, 14 Jul 2020 08:28:22: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:28:22: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Tue, 14 Jul 2020 08:28:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:28:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:28:23: 11000000 INFO @ Tue, 14 Jul 2020 08:28:29: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:28:34: 12000000 INFO @ Tue, 14 Jul 2020 08:28:37: 19000000 INFO @ Tue, 14 Jul 2020 08:28:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:28:45: 20000000 INFO @ Tue, 14 Jul 2020 08:28:45: 13000000 INFO @ Tue, 14 Jul 2020 08:28:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:28:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:28:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.05_summits.bed INFO @ Tue, 14 Jul 2020 08:28:46: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1103 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:28:53: 21000000 INFO @ Tue, 14 Jul 2020 08:28:54: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:28:54: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:28:54: #1 total tags in treatment: 8012718 INFO @ Tue, 14 Jul 2020 08:28:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:28:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:28:54: #1 tags after filtering in treatment: 7626302 INFO @ Tue, 14 Jul 2020 08:28:54: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 08:28:54: #1 finished! INFO @ Tue, 14 Jul 2020 08:28:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:28:54: 14000000 INFO @ Tue, 14 Jul 2020 08:28:55: #2 number of paired peaks: 244 WARNING @ Tue, 14 Jul 2020 08:28:55: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 14 Jul 2020 08:28:55: start model_add_line... INFO @ Tue, 14 Jul 2020 08:28:55: start X-correlation... INFO @ Tue, 14 Jul 2020 08:28:55: end of X-cor INFO @ Tue, 14 Jul 2020 08:28:55: #2 finished! INFO @ Tue, 14 Jul 2020 08:28:55: #2 predicted fragment length is 183 bps INFO @ Tue, 14 Jul 2020 08:28:55: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 14 Jul 2020 08:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.10_model.r WARNING @ Tue, 14 Jul 2020 08:28:55: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:28:55: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Tue, 14 Jul 2020 08:28:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:28:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:29:02: 15000000 INFO @ Tue, 14 Jul 2020 08:29:10: 16000000 INFO @ Tue, 14 Jul 2020 08:29:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:29:18: 17000000 INFO @ Tue, 14 Jul 2020 08:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.10_summits.bed INFO @ Tue, 14 Jul 2020 08:29:19: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (665 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:29:26: 18000000 INFO @ Tue, 14 Jul 2020 08:29:34: 19000000 INFO @ Tue, 14 Jul 2020 08:29:41: 20000000 INFO @ Tue, 14 Jul 2020 08:29:49: 21000000 INFO @ Tue, 14 Jul 2020 08:29:50: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:29:50: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:29:50: #1 total tags in treatment: 8012718 INFO @ Tue, 14 Jul 2020 08:29:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:29:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:29:50: #1 tags after filtering in treatment: 7626302 INFO @ Tue, 14 Jul 2020 08:29:50: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 08:29:50: #1 finished! INFO @ Tue, 14 Jul 2020 08:29:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:29:50: #2 number of paired peaks: 244 WARNING @ Tue, 14 Jul 2020 08:29:50: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 14 Jul 2020 08:29:50: start model_add_line... INFO @ Tue, 14 Jul 2020 08:29:50: start X-correlation... INFO @ Tue, 14 Jul 2020 08:29:50: end of X-cor INFO @ Tue, 14 Jul 2020 08:29:50: #2 finished! INFO @ Tue, 14 Jul 2020 08:29:50: #2 predicted fragment length is 183 bps INFO @ Tue, 14 Jul 2020 08:29:50: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 14 Jul 2020 08:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.20_model.r WARNING @ Tue, 14 Jul 2020 08:29:50: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:29:50: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Tue, 14 Jul 2020 08:29:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:29:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:30:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224576/SRX7224576.20_summits.bed INFO @ Tue, 14 Jul 2020 08:30:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling