Job ID = 14169841 SRX = SRX9910792 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36809121 spots for SRR13498863/SRR13498863.sra Written 36809121 spots for SRR13498863/SRR13498863.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170634 ("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: 01:17:07 36809121 reads; of these: 36809121 (100.00%) were paired; of these: 13985596 (37.99%) aligned concordantly 0 times 10554338 (28.67%) aligned concordantly exactly 1 time 12269187 (33.33%) aligned concordantly >1 times ---- 13985596 pairs aligned concordantly 0 times; of these: 1176672 (8.41%) aligned discordantly 1 time ---- 12808924 pairs aligned 0 times concordantly or discordantly; of these: 25617848 mates make up the pairs; of these: 19168818 (74.83%) aligned 0 times 412865 (1.61%) aligned exactly 1 time 6036165 (23.56%) aligned >1 times 73.96% overall alignment rate Time searching: 01:17:08 Overall time: 01:17:08 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 40 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] 13386065 / 23829745 = 0.5617 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 05:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.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 @ Sat, 11 Dec 2021 05:06:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:06:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:06:59: 1000000 INFO @ Sat, 11 Dec 2021 05:07:05: 2000000 INFO @ Sat, 11 Dec 2021 05:07:11: 3000000 INFO @ Sat, 11 Dec 2021 05:07:17: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 05:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.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 @ Sat, 11 Dec 2021 05:07:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:07:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:07:23: 5000000 INFO @ Sat, 11 Dec 2021 05:07:29: 1000000 INFO @ Sat, 11 Dec 2021 05:07:30: 6000000 INFO @ Sat, 11 Dec 2021 05:07:36: 2000000 INFO @ Sat, 11 Dec 2021 05:07:36: 7000000 INFO @ Sat, 11 Dec 2021 05:07:42: 3000000 INFO @ Sat, 11 Dec 2021 05:07:42: 8000000 INFO @ Sat, 11 Dec 2021 05:07:48: 4000000 INFO @ Sat, 11 Dec 2021 05:07:49: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 05:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.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 @ Sat, 11 Dec 2021 05:07:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:07:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:07:55: 5000000 INFO @ Sat, 11 Dec 2021 05:07:55: 10000000 INFO @ Sat, 11 Dec 2021 05:07:59: 1000000 INFO @ Sat, 11 Dec 2021 05:08:01: 6000000 INFO @ Sat, 11 Dec 2021 05:08:01: 11000000 INFO @ Sat, 11 Dec 2021 05:08:06: 2000000 INFO @ Sat, 11 Dec 2021 05:08:08: 7000000 INFO @ Sat, 11 Dec 2021 05:08:08: 12000000 INFO @ Sat, 11 Dec 2021 05:08:12: 3000000 INFO @ Sat, 11 Dec 2021 05:08:14: 8000000 INFO @ Sat, 11 Dec 2021 05:08:14: 13000000 INFO @ Sat, 11 Dec 2021 05:08:19: 4000000 INFO @ Sat, 11 Dec 2021 05:08:20: 9000000 INFO @ Sat, 11 Dec 2021 05:08:20: 14000000 INFO @ Sat, 11 Dec 2021 05:08:25: 5000000 INFO @ Sat, 11 Dec 2021 05:08:26: 10000000 INFO @ Sat, 11 Dec 2021 05:08:27: 15000000 INFO @ Sat, 11 Dec 2021 05:08:32: 6000000 INFO @ Sat, 11 Dec 2021 05:08:33: 11000000 INFO @ Sat, 11 Dec 2021 05:08:33: 16000000 INFO @ Sat, 11 Dec 2021 05:08:38: 7000000 INFO @ Sat, 11 Dec 2021 05:08:39: 17000000 INFO @ Sat, 11 Dec 2021 05:08:39: 12000000 INFO @ Sat, 11 Dec 2021 05:08:44: 8000000 INFO @ Sat, 11 Dec 2021 05:08:45: 18000000 INFO @ Sat, 11 Dec 2021 05:08:46: 13000000 INFO @ Sat, 11 Dec 2021 05:08:51: 9000000 INFO @ Sat, 11 Dec 2021 05:08:51: 19000000 INFO @ Sat, 11 Dec 2021 05:08:52: 14000000 INFO @ Sat, 11 Dec 2021 05:08:57: 10000000 INFO @ Sat, 11 Dec 2021 05:08:57: 20000000 INFO @ Sat, 11 Dec 2021 05:08:58: 15000000 INFO @ Sat, 11 Dec 2021 05:09:03: 21000000 INFO @ Sat, 11 Dec 2021 05:09:03: 11000000 INFO @ Sat, 11 Dec 2021 05:09:05: 16000000 INFO @ Sat, 11 Dec 2021 05:09:09: 22000000 INFO @ Sat, 11 Dec 2021 05:09:10: 12000000 INFO @ Sat, 11 Dec 2021 05:09:11: 17000000 INFO @ Sat, 11 Dec 2021 05:09:15: 23000000 INFO @ Sat, 11 Dec 2021 05:09:16: 13000000 INFO @ Sat, 11 Dec 2021 05:09:17: 18000000 INFO @ Sat, 11 Dec 2021 05:09:22: 24000000 INFO @ Sat, 11 Dec 2021 05:09:23: 14000000 INFO @ Sat, 11 Dec 2021 05:09:23: 19000000 INFO @ Sat, 11 Dec 2021 05:09:28: 25000000 INFO @ Sat, 11 Dec 2021 05:09:29: 20000000 INFO @ Sat, 11 Dec 2021 05:09:29: 15000000 INFO @ Sat, 11 Dec 2021 05:09:35: 26000000 INFO @ Sat, 11 Dec 2021 05:09:35: 21000000 INFO @ Sat, 11 Dec 2021 05:09:35: 16000000 INFO @ Sat, 11 Dec 2021 05:09:41: 27000000 INFO @ Sat, 11 Dec 2021 05:09:41: 22000000 INFO @ Sat, 11 Dec 2021 05:09:41: 17000000 INFO @ Sat, 11 Dec 2021 05:09:46: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 05:09:46: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 05:09:46: #1 total tags in treatment: 9832618 INFO @ Sat, 11 Dec 2021 05:09:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:09:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 05:09:46: #1 tags after filtering in treatment: 7443518 INFO @ Sat, 11 Dec 2021 05:09:46: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 05:09:46: #1 finished! INFO @ Sat, 11 Dec 2021 05:09:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:09:46: #2 number of paired peaks: 443 WARNING @ Sat, 11 Dec 2021 05:09:46: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sat, 11 Dec 2021 05:09:46: start model_add_line... INFO @ Sat, 11 Dec 2021 05:09:46: start X-correlation... INFO @ Sat, 11 Dec 2021 05:09:46: end of X-cor INFO @ Sat, 11 Dec 2021 05:09:46: #2 finished! INFO @ Sat, 11 Dec 2021 05:09:46: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 05:09:46: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 05:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.05_model.r WARNING @ Sat, 11 Dec 2021 05:09:46: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:09:46: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 11 Dec 2021 05:09:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 05:09:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:09:47: 23000000 INFO @ Sat, 11 Dec 2021 05:09:47: 18000000 INFO @ Sat, 11 Dec 2021 05:09:53: 19000000 INFO @ Sat, 11 Dec 2021 05:09:54: 24000000 INFO @ Sat, 11 Dec 2021 05:10:00: 20000000 INFO @ Sat, 11 Dec 2021 05:10:00: 25000000 INFO @ Sat, 11 Dec 2021 05:10:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:10:06: 21000000 INFO @ Sat, 11 Dec 2021 05:10:07: 26000000 INFO @ Sat, 11 Dec 2021 05:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.05_peaks.xls INFO @ Sat, 11 Dec 2021 05:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.05_summits.bed INFO @ Sat, 11 Dec 2021 05:10:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4231 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 05:10:12: 22000000 INFO @ Sat, 11 Dec 2021 05:10:13: 27000000 INFO @ Sat, 11 Dec 2021 05:10:17: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 05:10:17: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 05:10:17: #1 total tags in treatment: 9832618 INFO @ Sat, 11 Dec 2021 05:10:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:10:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 05:10:18: #1 tags after filtering in treatment: 7443518 INFO @ Sat, 11 Dec 2021 05:10:18: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 05:10:18: #1 finished! INFO @ Sat, 11 Dec 2021 05:10:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:10:18: 23000000 INFO @ Sat, 11 Dec 2021 05:10:18: #2 number of paired peaks: 443 WARNING @ Sat, 11 Dec 2021 05:10:18: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sat, 11 Dec 2021 05:10:18: start model_add_line... INFO @ Sat, 11 Dec 2021 05:10:18: start X-correlation... INFO @ Sat, 11 Dec 2021 05:10:18: end of X-cor INFO @ Sat, 11 Dec 2021 05:10:18: #2 finished! INFO @ Sat, 11 Dec 2021 05:10:18: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 05:10:18: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 05:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.10_model.r WARNING @ Sat, 11 Dec 2021 05:10:18: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:10:18: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 11 Dec 2021 05:10:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 05:10:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:10:24: 24000000 INFO @ Sat, 11 Dec 2021 05:10:30: 25000000 INFO @ Sat, 11 Dec 2021 05:10:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:10:36: 26000000 INFO @ Sat, 11 Dec 2021 05:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.10_peaks.xls INFO @ Sat, 11 Dec 2021 05:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.10_summits.bed INFO @ Sat, 11 Dec 2021 05:10:42: Done! INFO @ Sat, 11 Dec 2021 05:10:43: 27000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1441 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 05:10:47: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 05:10:47: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 05:10:47: #1 total tags in treatment: 9832618 INFO @ Sat, 11 Dec 2021 05:10:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:10:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 05:10:47: #1 tags after filtering in treatment: 7443518 INFO @ Sat, 11 Dec 2021 05:10:47: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 05:10:47: #1 finished! INFO @ Sat, 11 Dec 2021 05:10:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:10:48: #2 number of paired peaks: 443 WARNING @ Sat, 11 Dec 2021 05:10:48: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sat, 11 Dec 2021 05:10:48: start model_add_line... INFO @ Sat, 11 Dec 2021 05:10:48: start X-correlation... INFO @ Sat, 11 Dec 2021 05:10:48: end of X-cor INFO @ Sat, 11 Dec 2021 05:10:48: #2 finished! INFO @ Sat, 11 Dec 2021 05:10:48: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 05:10:48: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 05:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.20_model.r WARNING @ Sat, 11 Dec 2021 05:10:48: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:10:48: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 11 Dec 2021 05:10:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 05:10:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:11:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.20_peaks.xls INFO @ Sat, 11 Dec 2021 05:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910792/SRX9910792.20_summits.bed INFO @ Sat, 11 Dec 2021 05:11:14: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (374 records, 4 fields): 2 millis CompletedMACS2peakCalling