Job ID = 6626495 SRX = SRX5736474 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12187534 spots for SRR8956885/SRR8956885.sra Written 12187534 spots for SRR8956885/SRR8956885.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626713 ("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: 00:36:44 12187534 reads; of these: 12187534 (100.00%) were paired; of these: 1019270 (8.36%) aligned concordantly 0 times 7306612 (59.95%) aligned concordantly exactly 1 time 3861652 (31.69%) aligned concordantly >1 times ---- 1019270 pairs aligned concordantly 0 times; of these: 197295 (19.36%) aligned discordantly 1 time ---- 821975 pairs aligned 0 times concordantly or discordantly; of these: 1643950 mates make up the pairs; of these: 1093005 (66.49%) aligned 0 times 264322 (16.08%) aligned exactly 1 time 286623 (17.44%) aligned >1 times 95.52% overall alignment rate Time searching: 00:36:44 Overall time: 00:36:44 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 12 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] 1123798 / 11337256 = 0.0991 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 07:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.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 07:52:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:52:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:52:08: 1000000 INFO @ Tue, 14 Jul 2020 07:52:13: 2000000 INFO @ Tue, 14 Jul 2020 07:52:18: 3000000 INFO @ Tue, 14 Jul 2020 07:52:23: 4000000 INFO @ Tue, 14 Jul 2020 07:52:28: 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 @ Tue, 14 Jul 2020 07:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.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 07:52:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:52:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:52:33: 6000000 INFO @ Tue, 14 Jul 2020 07:52:38: 1000000 INFO @ Tue, 14 Jul 2020 07:52:38: 7000000 INFO @ Tue, 14 Jul 2020 07:52:43: 2000000 INFO @ Tue, 14 Jul 2020 07:52:43: 8000000 INFO @ Tue, 14 Jul 2020 07:52:48: 3000000 INFO @ Tue, 14 Jul 2020 07:52:49: 9000000 INFO @ Tue, 14 Jul 2020 07:52:53: 4000000 INFO @ Tue, 14 Jul 2020 07:52:54: 10000000 INFO @ Tue, 14 Jul 2020 07:52:58: 5000000 INFO @ Tue, 14 Jul 2020 07:52:59: 11000000 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 07:53:03: 6000000 INFO @ Tue, 14 Jul 2020 07:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.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 07:53:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:53:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:53:04: 12000000 INFO @ Tue, 14 Jul 2020 07:53:08: 7000000 INFO @ Tue, 14 Jul 2020 07:53:08: 1000000 INFO @ Tue, 14 Jul 2020 07:53:09: 13000000 INFO @ Tue, 14 Jul 2020 07:53:13: 8000000 INFO @ Tue, 14 Jul 2020 07:53:13: 2000000 INFO @ Tue, 14 Jul 2020 07:53:15: 14000000 INFO @ Tue, 14 Jul 2020 07:53:18: 9000000 INFO @ Tue, 14 Jul 2020 07:53:18: 3000000 INFO @ Tue, 14 Jul 2020 07:53:20: 15000000 INFO @ Tue, 14 Jul 2020 07:53:23: 10000000 INFO @ Tue, 14 Jul 2020 07:53:23: 4000000 INFO @ Tue, 14 Jul 2020 07:53:25: 16000000 INFO @ Tue, 14 Jul 2020 07:53:28: 11000000 INFO @ Tue, 14 Jul 2020 07:53:28: 5000000 INFO @ Tue, 14 Jul 2020 07:53:30: 17000000 INFO @ Tue, 14 Jul 2020 07:53:33: 12000000 INFO @ Tue, 14 Jul 2020 07:53:33: 6000000 INFO @ Tue, 14 Jul 2020 07:53:36: 18000000 INFO @ Tue, 14 Jul 2020 07:53:38: 13000000 INFO @ Tue, 14 Jul 2020 07:53:38: 7000000 INFO @ Tue, 14 Jul 2020 07:53:41: 19000000 INFO @ Tue, 14 Jul 2020 07:53:44: 14000000 INFO @ Tue, 14 Jul 2020 07:53:44: 8000000 INFO @ Tue, 14 Jul 2020 07:53:47: 20000000 INFO @ Tue, 14 Jul 2020 07:53:49: 9000000 INFO @ Tue, 14 Jul 2020 07:53:49: 15000000 INFO @ Tue, 14 Jul 2020 07:53:52: 21000000 INFO @ Tue, 14 Jul 2020 07:53:52: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:53:52: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:53:52: #1 total tags in treatment: 10064050 INFO @ Tue, 14 Jul 2020 07:53:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:53:52: #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 07:53:53: #1 tags after filtering in treatment: 9231899 INFO @ Tue, 14 Jul 2020 07:53:53: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:53:53: #1 finished! INFO @ Tue, 14 Jul 2020 07:53:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:53:53: #2 number of paired peaks: 161 WARNING @ Tue, 14 Jul 2020 07:53:53: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 14 Jul 2020 07:53:53: start model_add_line... INFO @ Tue, 14 Jul 2020 07:53:53: start X-correlation... INFO @ Tue, 14 Jul 2020 07:53:53: end of X-cor INFO @ Tue, 14 Jul 2020 07:53:53: #2 finished! INFO @ Tue, 14 Jul 2020 07:53:53: #2 predicted fragment length is 140 bps INFO @ Tue, 14 Jul 2020 07:53:53: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 14 Jul 2020 07:53:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.05_model.r WARNING @ Tue, 14 Jul 2020 07:53:53: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:53:53: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Tue, 14 Jul 2020 07:53:53: #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 07:53:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:53:54: 10000000 INFO @ Tue, 14 Jul 2020 07:53:54: 16000000 INFO @ Tue, 14 Jul 2020 07:53:59: 11000000 INFO @ Tue, 14 Jul 2020 07:53:59: 17000000 INFO @ Tue, 14 Jul 2020 07:54:04: 18000000 INFO @ Tue, 14 Jul 2020 07:54:04: 12000000 INFO @ Tue, 14 Jul 2020 07:54:09: 19000000 INFO @ Tue, 14 Jul 2020 07:54:09: 13000000 INFO @ Tue, 14 Jul 2020 07:54:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:54:14: 20000000 INFO @ Tue, 14 Jul 2020 07:54:14: 14000000 INFO @ Tue, 14 Jul 2020 07:54:20: 21000000 INFO @ Tue, 14 Jul 2020 07:54:20: 15000000 INFO @ Tue, 14 Jul 2020 07:54:20: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:54:20: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:54:20: #1 total tags in treatment: 10064050 INFO @ Tue, 14 Jul 2020 07:54:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:54:20: #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 07:54:20: #1 tags after filtering in treatment: 9231899 INFO @ Tue, 14 Jul 2020 07:54:20: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:54:20: #1 finished! INFO @ Tue, 14 Jul 2020 07:54:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:54:21: #2 number of paired peaks: 161 WARNING @ Tue, 14 Jul 2020 07:54:21: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 14 Jul 2020 07:54:21: start model_add_line... INFO @ Tue, 14 Jul 2020 07:54:21: start X-correlation... INFO @ Tue, 14 Jul 2020 07:54:21: end of X-cor INFO @ Tue, 14 Jul 2020 07:54:21: #2 finished! INFO @ Tue, 14 Jul 2020 07:54:21: #2 predicted fragment length is 140 bps INFO @ Tue, 14 Jul 2020 07:54:21: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 14 Jul 2020 07:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.10_model.r WARNING @ Tue, 14 Jul 2020 07:54:21: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:54:21: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Tue, 14 Jul 2020 07:54:21: #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 07:54:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:54:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:54:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.05_summits.bed INFO @ Tue, 14 Jul 2020 07:54:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3383 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:54:25: 16000000 INFO @ Tue, 14 Jul 2020 07:54:30: 17000000 INFO @ Tue, 14 Jul 2020 07:54:35: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:54:39: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:54:40: 19000000 INFO @ Tue, 14 Jul 2020 07:54:45: 20000000 INFO @ Tue, 14 Jul 2020 07:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.10_summits.bed INFO @ Tue, 14 Jul 2020 07:54:49: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1007 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:54:50: 21000000 INFO @ Tue, 14 Jul 2020 07:54:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:54:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:54:50: #1 total tags in treatment: 10064050 INFO @ Tue, 14 Jul 2020 07:54:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:54:50: #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 07:54:50: #1 tags after filtering in treatment: 9231899 INFO @ Tue, 14 Jul 2020 07:54:50: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:54:50: #1 finished! INFO @ Tue, 14 Jul 2020 07:54:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:54:51: #2 number of paired peaks: 161 WARNING @ Tue, 14 Jul 2020 07:54:51: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 14 Jul 2020 07:54:51: start model_add_line... INFO @ Tue, 14 Jul 2020 07:54:51: start X-correlation... INFO @ Tue, 14 Jul 2020 07:54:51: end of X-cor INFO @ Tue, 14 Jul 2020 07:54:51: #2 finished! INFO @ Tue, 14 Jul 2020 07:54:51: #2 predicted fragment length is 140 bps INFO @ Tue, 14 Jul 2020 07:54:51: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 14 Jul 2020 07:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.20_model.r WARNING @ Tue, 14 Jul 2020 07:54:51: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:54:51: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Tue, 14 Jul 2020 07:54:51: #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 07:54:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:55:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736474/SRX5736474.20_summits.bed INFO @ Tue, 14 Jul 2020 07:55:19: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 13 millis CompletedMACS2peakCalling