Job ID = 14172074 SRX = SRX10386199 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19087988 spots for SRR14009264/SRR14009264.sra Written 19087988 spots for SRR14009264/SRR14009264.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172661 ("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: 00:46:26 19087988 reads; of these: 19087988 (100.00%) were paired; of these: 5365306 (28.11%) aligned concordantly 0 times 8732295 (45.75%) aligned concordantly exactly 1 time 4990387 (26.14%) aligned concordantly >1 times ---- 5365306 pairs aligned concordantly 0 times; of these: 147190 (2.74%) aligned discordantly 1 time ---- 5218116 pairs aligned 0 times concordantly or discordantly; of these: 10436232 mates make up the pairs; of these: 9628321 (92.26%) aligned 0 times 449163 (4.30%) aligned exactly 1 time 358748 (3.44%) aligned >1 times 74.78% overall alignment rate Time searching: 00:46:26 Overall time: 00:46:26 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] 3552794 / 13833865 = 0.2568 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 14:56:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.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 14:56:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:56:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:56:44: 1000000 INFO @ Sat, 11 Dec 2021 14:56:52: 2000000 INFO @ Sat, 11 Dec 2021 14:56:59: 3000000 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 14:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.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 14:57:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:57:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:57:08: 4000000 INFO @ Sat, 11 Dec 2021 14:57:15: 1000000 INFO @ Sat, 11 Dec 2021 14:57:16: 5000000 INFO @ Sat, 11 Dec 2021 14:57:24: 6000000 INFO @ Sat, 11 Dec 2021 14:57:25: 2000000 INFO @ Sat, 11 Dec 2021 14:57:32: 7000000 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 14:57:34: 3000000 INFO @ Sat, 11 Dec 2021 14:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.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 14:57:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:57:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:57:40: 8000000 INFO @ Sat, 11 Dec 2021 14:57:44: 4000000 INFO @ Sat, 11 Dec 2021 14:57:44: 1000000 INFO @ Sat, 11 Dec 2021 14:57:48: 9000000 INFO @ Sat, 11 Dec 2021 14:57:52: 2000000 INFO @ Sat, 11 Dec 2021 14:57:54: 5000000 INFO @ Sat, 11 Dec 2021 14:57:57: 10000000 INFO @ Sat, 11 Dec 2021 14:58:01: 3000000 INFO @ Sat, 11 Dec 2021 14:58:03: 6000000 INFO @ Sat, 11 Dec 2021 14:58:05: 11000000 INFO @ Sat, 11 Dec 2021 14:58:09: 4000000 INFO @ Sat, 11 Dec 2021 14:58:13: 7000000 INFO @ Sat, 11 Dec 2021 14:58:13: 12000000 INFO @ Sat, 11 Dec 2021 14:58:17: 5000000 INFO @ Sat, 11 Dec 2021 14:58:22: 13000000 INFO @ Sat, 11 Dec 2021 14:58:23: 8000000 INFO @ Sat, 11 Dec 2021 14:58:25: 6000000 INFO @ Sat, 11 Dec 2021 14:58:30: 14000000 INFO @ Sat, 11 Dec 2021 14:58:33: 9000000 INFO @ Sat, 11 Dec 2021 14:58:34: 7000000 INFO @ Sat, 11 Dec 2021 14:58:38: 15000000 INFO @ Sat, 11 Dec 2021 14:58:42: 8000000 INFO @ Sat, 11 Dec 2021 14:58:42: 10000000 INFO @ Sat, 11 Dec 2021 14:58:46: 16000000 INFO @ Sat, 11 Dec 2021 14:58:50: 9000000 INFO @ Sat, 11 Dec 2021 14:58:52: 11000000 INFO @ Sat, 11 Dec 2021 14:58:54: 17000000 INFO @ Sat, 11 Dec 2021 14:58:59: 10000000 INFO @ Sat, 11 Dec 2021 14:59:02: 12000000 INFO @ Sat, 11 Dec 2021 14:59:02: 18000000 INFO @ Sat, 11 Dec 2021 14:59:07: 11000000 INFO @ Sat, 11 Dec 2021 14:59:10: 19000000 INFO @ Sat, 11 Dec 2021 14:59:11: 13000000 INFO @ Sat, 11 Dec 2021 14:59:16: 12000000 INFO @ Sat, 11 Dec 2021 14:59:18: 20000000 INFO @ Sat, 11 Dec 2021 14:59:21: 14000000 INFO @ Sat, 11 Dec 2021 14:59:24: 13000000 INFO @ Sat, 11 Dec 2021 14:59:26: 21000000 INFO @ Sat, 11 Dec 2021 14:59:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:59:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:59:30: #1 total tags in treatment: 10192103 INFO @ Sat, 11 Dec 2021 14:59:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:59:30: #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 14:59:30: #1 tags after filtering in treatment: 8646404 INFO @ Sat, 11 Dec 2021 14:59:30: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 14:59:30: #1 finished! INFO @ Sat, 11 Dec 2021 14:59:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:59:31: #2 number of paired peaks: 314 WARNING @ Sat, 11 Dec 2021 14:59:31: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sat, 11 Dec 2021 14:59:31: start model_add_line... INFO @ Sat, 11 Dec 2021 14:59:31: start X-correlation... INFO @ Sat, 11 Dec 2021 14:59:31: 15000000 INFO @ Sat, 11 Dec 2021 14:59:31: end of X-cor INFO @ Sat, 11 Dec 2021 14:59:31: #2 finished! INFO @ Sat, 11 Dec 2021 14:59:31: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Dec 2021 14:59:31: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Dec 2021 14:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.05_model.r WARNING @ Sat, 11 Dec 2021 14:59:31: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:59:31: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 11 Dec 2021 14:59:31: #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 14:59:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:59:32: 14000000 INFO @ Sat, 11 Dec 2021 14:59:40: 16000000 INFO @ Sat, 11 Dec 2021 14:59:40: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:59:48: 16000000 INFO @ Sat, 11 Dec 2021 14:59:49: 17000000 INFO @ Sat, 11 Dec 2021 14:59:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:59:56: 17000000 INFO @ Sat, 11 Dec 2021 14:59:58: 18000000 INFO @ Sat, 11 Dec 2021 15:00:04: 18000000 INFO @ Sat, 11 Dec 2021 15:00:07: 19000000 INFO @ Sat, 11 Dec 2021 15:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.05_summits.bed INFO @ Sat, 11 Dec 2021 15:00:08: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1635 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:00:12: 19000000 INFO @ Sat, 11 Dec 2021 15:00:16: 20000000 INFO @ Sat, 11 Dec 2021 15:00:20: 20000000 INFO @ Sat, 11 Dec 2021 15:00:25: 21000000 INFO @ Sat, 11 Dec 2021 15:00:28: 21000000 INFO @ Sat, 11 Dec 2021 15:00:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:00:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:00:29: #1 total tags in treatment: 10192103 INFO @ Sat, 11 Dec 2021 15:00:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:29: #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 15:00:30: #1 tags after filtering in treatment: 8646404 INFO @ Sat, 11 Dec 2021 15:00:30: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:00:30: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:30: #2 number of paired peaks: 314 WARNING @ Sat, 11 Dec 2021 15:00:30: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sat, 11 Dec 2021 15:00:30: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:30: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:30: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:30: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:30: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Dec 2021 15:00:30: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Dec 2021 15:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.10_model.r WARNING @ Sat, 11 Dec 2021 15:00:30: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:00:30: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 11 Dec 2021 15:00:30: #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 15:00:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:00:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:00:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:00:32: #1 total tags in treatment: 10192103 INFO @ Sat, 11 Dec 2021 15:00:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:32: #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 15:00:32: #1 tags after filtering in treatment: 8646404 INFO @ Sat, 11 Dec 2021 15:00:32: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:00:32: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:33: #2 number of paired peaks: 314 WARNING @ Sat, 11 Dec 2021 15:00:33: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sat, 11 Dec 2021 15:00:33: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:33: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:33: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:33: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:33: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Dec 2021 15:00:33: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Dec 2021 15:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.20_model.r WARNING @ Sat, 11 Dec 2021 15:00:33: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:00:33: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 11 Dec 2021 15:00:33: #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 15:00:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:00:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.10_summits.bed INFO @ Sat, 11 Dec 2021 15:01:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1001 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386199/SRX10386199.20_summits.bed INFO @ Sat, 11 Dec 2021 15:01:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (624 records, 4 fields): 2 millis CompletedMACS2peakCalling