Job ID = 16439431 SRX = SRX11245087 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24213858 spots for SRR14932352/SRR14932352.sra Written 24213858 spots for SRR14932352/SRR14932352.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440040 ("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: 01:28:23 24213858 reads; of these: 24213858 (100.00%) were paired; of these: 10178377 (42.04%) aligned concordantly 0 times 11421390 (47.17%) aligned concordantly exactly 1 time 2614091 (10.80%) aligned concordantly >1 times ---- 10178377 pairs aligned concordantly 0 times; of these: 2387281 (23.45%) aligned discordantly 1 time ---- 7791096 pairs aligned 0 times concordantly or discordantly; of these: 15582192 mates make up the pairs; of these: 13800226 (88.56%) aligned 0 times 645574 (4.14%) aligned exactly 1 time 1136392 (7.29%) aligned >1 times 71.50% overall alignment rate Time searching: 01:28:23 Overall time: 01:28:23 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 28 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] 6323504 / 16376155 = 0.3861 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.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, 02 Aug 2022 16:56:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:56:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:56:10: 1000000 INFO @ Tue, 02 Aug 2022 16:56:20: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.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, 02 Aug 2022 16:56:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:56:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:56:30: 3000000 INFO @ Tue, 02 Aug 2022 16:56:39: 1000000 INFO @ Tue, 02 Aug 2022 16:56:40: 4000000 INFO @ Tue, 02 Aug 2022 16:56:49: 2000000 INFO @ Tue, 02 Aug 2022 16:56:49: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:56:58: 3000000 INFO @ Tue, 02 Aug 2022 16:56:59: 6000000 INFO @ Tue, 02 Aug 2022 16:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.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, 02 Aug 2022 16:57:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:57:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:57:08: 4000000 INFO @ Tue, 02 Aug 2022 16:57:09: 7000000 INFO @ Tue, 02 Aug 2022 16:57:10: 1000000 INFO @ Tue, 02 Aug 2022 16:57:17: 5000000 INFO @ Tue, 02 Aug 2022 16:57:20: 8000000 INFO @ Tue, 02 Aug 2022 16:57:21: 2000000 INFO @ Tue, 02 Aug 2022 16:57:26: 6000000 INFO @ Tue, 02 Aug 2022 16:57:30: 9000000 INFO @ Tue, 02 Aug 2022 16:57:31: 3000000 INFO @ Tue, 02 Aug 2022 16:57:36: 7000000 INFO @ Tue, 02 Aug 2022 16:57:40: 10000000 INFO @ Tue, 02 Aug 2022 16:57:41: 4000000 INFO @ Tue, 02 Aug 2022 16:57:45: 8000000 INFO @ Tue, 02 Aug 2022 16:57:51: 11000000 INFO @ Tue, 02 Aug 2022 16:57:51: 5000000 INFO @ Tue, 02 Aug 2022 16:57:55: 9000000 INFO @ Tue, 02 Aug 2022 16:58:01: 12000000 INFO @ Tue, 02 Aug 2022 16:58:02: 6000000 INFO @ Tue, 02 Aug 2022 16:58:05: 10000000 INFO @ Tue, 02 Aug 2022 16:58:11: 13000000 INFO @ Tue, 02 Aug 2022 16:58:13: 7000000 INFO @ Tue, 02 Aug 2022 16:58:15: 11000000 INFO @ Tue, 02 Aug 2022 16:58:20: 14000000 INFO @ Tue, 02 Aug 2022 16:58:23: 8000000 INFO @ Tue, 02 Aug 2022 16:58:24: 12000000 INFO @ Tue, 02 Aug 2022 16:58:30: 15000000 INFO @ Tue, 02 Aug 2022 16:58:33: 13000000 INFO @ Tue, 02 Aug 2022 16:58:33: 9000000 INFO @ Tue, 02 Aug 2022 16:58:40: 16000000 INFO @ Tue, 02 Aug 2022 16:58:42: 14000000 INFO @ Tue, 02 Aug 2022 16:58:43: 10000000 INFO @ Tue, 02 Aug 2022 16:58:50: 17000000 INFO @ Tue, 02 Aug 2022 16:58:51: 15000000 INFO @ Tue, 02 Aug 2022 16:58:53: 11000000 INFO @ Tue, 02 Aug 2022 16:59:00: 16000000 INFO @ Tue, 02 Aug 2022 16:59:01: 18000000 INFO @ Tue, 02 Aug 2022 16:59:02: 12000000 INFO @ Tue, 02 Aug 2022 16:59:10: 17000000 INFO @ Tue, 02 Aug 2022 16:59:11: 19000000 INFO @ Tue, 02 Aug 2022 16:59:12: 13000000 INFO @ Tue, 02 Aug 2022 16:59:19: 18000000 INFO @ Tue, 02 Aug 2022 16:59:21: 20000000 INFO @ Tue, 02 Aug 2022 16:59:22: 14000000 INFO @ Tue, 02 Aug 2022 16:59:28: 19000000 INFO @ Tue, 02 Aug 2022 16:59:31: 21000000 INFO @ Tue, 02 Aug 2022 16:59:32: 15000000 INFO @ Tue, 02 Aug 2022 16:59:38: 20000000 INFO @ Tue, 02 Aug 2022 16:59:41: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:59:41: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:59:41: #1 total tags in treatment: 8699851 INFO @ Tue, 02 Aug 2022 16:59:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:59:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:59:41: 16000000 INFO @ Tue, 02 Aug 2022 16:59:42: #1 tags after filtering in treatment: 8358739 INFO @ Tue, 02 Aug 2022 16:59:42: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 16:59:42: #1 finished! INFO @ Tue, 02 Aug 2022 16:59:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:59:42: #2 number of paired peaks: 185 WARNING @ Tue, 02 Aug 2022 16:59:42: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 02 Aug 2022 16:59:42: start model_add_line... INFO @ Tue, 02 Aug 2022 16:59:42: start X-correlation... INFO @ Tue, 02 Aug 2022 16:59:42: end of X-cor INFO @ Tue, 02 Aug 2022 16:59:42: #2 finished! INFO @ Tue, 02 Aug 2022 16:59:42: #2 predicted fragment length is 196 bps INFO @ Tue, 02 Aug 2022 16:59:42: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 02 Aug 2022 16:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.05_model.r WARNING @ Tue, 02 Aug 2022 16:59:43: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:59:43: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 02 Aug 2022 16:59:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:59:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:59:47: 21000000 INFO @ Tue, 02 Aug 2022 16:59:51: 17000000 INFO @ Tue, 02 Aug 2022 16:59:56: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:59:56: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:59:56: #1 total tags in treatment: 8699851 INFO @ Tue, 02 Aug 2022 16:59:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:59:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:59:56: #1 tags after filtering in treatment: 8358739 INFO @ Tue, 02 Aug 2022 16:59:56: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 16:59:56: #1 finished! INFO @ Tue, 02 Aug 2022 16:59:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:59:57: #2 number of paired peaks: 185 WARNING @ Tue, 02 Aug 2022 16:59:57: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 02 Aug 2022 16:59:57: start model_add_line... INFO @ Tue, 02 Aug 2022 16:59:57: start X-correlation... INFO @ Tue, 02 Aug 2022 16:59:57: end of X-cor INFO @ Tue, 02 Aug 2022 16:59:57: #2 finished! INFO @ Tue, 02 Aug 2022 16:59:57: #2 predicted fragment length is 196 bps INFO @ Tue, 02 Aug 2022 16:59:57: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 02 Aug 2022 16:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.10_model.r WARNING @ Tue, 02 Aug 2022 16:59:57: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:59:57: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 02 Aug 2022 16:59:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:59:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:59:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:00:00: 18000000 INFO @ Tue, 02 Aug 2022 17:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.05_summits.bed INFO @ Tue, 02 Aug 2022 17:00:08: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:00:10: 19000000 INFO @ Tue, 02 Aug 2022 17:00:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:00:19: 20000000 INFO @ Tue, 02 Aug 2022 17:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.10_summits.bed INFO @ Tue, 02 Aug 2022 17:00:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 77 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:00:29: 21000000 INFO @ Tue, 02 Aug 2022 17:00:38: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:00:38: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:00:38: #1 total tags in treatment: 8699851 INFO @ Tue, 02 Aug 2022 17:00:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:00:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:00:38: #1 tags after filtering in treatment: 8358739 INFO @ Tue, 02 Aug 2022 17:00:38: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 17:00:38: #1 finished! INFO @ Tue, 02 Aug 2022 17:00:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:00:38: #2 number of paired peaks: 185 WARNING @ Tue, 02 Aug 2022 17:00:38: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 02 Aug 2022 17:00:38: start model_add_line... INFO @ Tue, 02 Aug 2022 17:00:38: start X-correlation... INFO @ Tue, 02 Aug 2022 17:00:38: end of X-cor INFO @ Tue, 02 Aug 2022 17:00:38: #2 finished! INFO @ Tue, 02 Aug 2022 17:00:38: #2 predicted fragment length is 196 bps INFO @ Tue, 02 Aug 2022 17:00:38: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 02 Aug 2022 17:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.20_model.r WARNING @ Tue, 02 Aug 2022 17:00:38: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:00:38: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 02 Aug 2022 17:00:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:00:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:00:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245087/SRX11245087.20_summits.bed INFO @ Tue, 02 Aug 2022 17:01:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (457 records, 4 fields): 59 millis CompletedMACS2peakCalling BigWig に変換しました。