Job ID = 16439404 SRX = SRX11245072 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:04:21 prefetch.2.10.7: 1) Downloading 'SRR14932337'... 2022-08-02T06:04:21 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:04:42 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:04:42 prefetch.2.10.7: 1) 'SRR14932337' was downloaded successfully 2022-08-02T06:04:42 prefetch.2.10.7: 'SRR14932337' has 0 unresolved dependencies Read 9918912 spots for SRR14932337/SRR14932337.sra Written 9918912 spots for SRR14932337/SRR14932337.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439655 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:40:02 9918912 reads; of these: 9918912 (100.00%) were paired; of these: 2684696 (27.07%) aligned concordantly 0 times 5091680 (51.33%) aligned concordantly exactly 1 time 2142536 (21.60%) aligned concordantly >1 times ---- 2684696 pairs aligned concordantly 0 times; of these: 974992 (36.32%) aligned discordantly 1 time ---- 1709704 pairs aligned 0 times concordantly or discordantly; of these: 3419408 mates make up the pairs; of these: 2410643 (70.50%) aligned 0 times 262580 (7.68%) aligned exactly 1 time 746185 (21.82%) aligned >1 times 87.85% overall alignment rate Time searching: 00:40:03 Overall time: 00:40:03 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 16 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] 1785321 / 8154792 = 0.2189 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 15:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.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 15:52:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:52:31: 1000000 INFO @ Tue, 02 Aug 2022 15:52:38: 2000000 INFO @ Tue, 02 Aug 2022 15:52:45: 3000000 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 15:52:53: 4000000 INFO @ Tue, 02 Aug 2022 15:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.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 15:52:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:00: 5000000 INFO @ Tue, 02 Aug 2022 15:53:02: 1000000 INFO @ Tue, 02 Aug 2022 15:53:07: 6000000 INFO @ Tue, 02 Aug 2022 15:53:09: 2000000 INFO @ Tue, 02 Aug 2022 15:53:15: 7000000 INFO @ Tue, 02 Aug 2022 15:53:17: 3000000 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 15:53:22: 8000000 INFO @ Tue, 02 Aug 2022 15:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.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 15:53:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:53:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:25: 4000000 INFO @ Tue, 02 Aug 2022 15:53:30: 9000000 INFO @ Tue, 02 Aug 2022 15:53:32: 1000000 INFO @ Tue, 02 Aug 2022 15:53:32: 5000000 INFO @ Tue, 02 Aug 2022 15:53:37: 10000000 INFO @ Tue, 02 Aug 2022 15:53:39: 6000000 INFO @ Tue, 02 Aug 2022 15:53:39: 2000000 INFO @ Tue, 02 Aug 2022 15:53:45: 11000000 INFO @ Tue, 02 Aug 2022 15:53:46: 7000000 INFO @ Tue, 02 Aug 2022 15:53:46: 3000000 INFO @ Tue, 02 Aug 2022 15:53:52: 8000000 INFO @ Tue, 02 Aug 2022 15:53:53: 12000000 INFO @ Tue, 02 Aug 2022 15:53:54: 4000000 INFO @ Tue, 02 Aug 2022 15:53:59: 9000000 INFO @ Tue, 02 Aug 2022 15:54:01: 13000000 INFO @ Tue, 02 Aug 2022 15:54:01: 5000000 INFO @ Tue, 02 Aug 2022 15:54:06: 10000000 INFO @ Tue, 02 Aug 2022 15:54:07: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:54:07: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:54:07: #1 total tags in treatment: 5656915 INFO @ Tue, 02 Aug 2022 15:54:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:54:07: #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 15:54:07: #1 tags after filtering in treatment: 5445877 INFO @ Tue, 02 Aug 2022 15:54:07: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:54:07: #1 finished! INFO @ Tue, 02 Aug 2022 15:54:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:54:08: #2 number of paired peaks: 346 WARNING @ Tue, 02 Aug 2022 15:54:08: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 02 Aug 2022 15:54:08: start model_add_line... INFO @ Tue, 02 Aug 2022 15:54:08: start X-correlation... INFO @ Tue, 02 Aug 2022 15:54:08: end of X-cor INFO @ Tue, 02 Aug 2022 15:54:08: #2 finished! INFO @ Tue, 02 Aug 2022 15:54:08: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 15:54:08: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 15:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.05_model.r WARNING @ Tue, 02 Aug 2022 15:54:08: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:54:08: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Tue, 02 Aug 2022 15:54:08: #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 15:54:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:54:08: 6000000 INFO @ Tue, 02 Aug 2022 15:54:14: 11000000 INFO @ Tue, 02 Aug 2022 15:54:16: 7000000 INFO @ Tue, 02 Aug 2022 15:54:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:22: 12000000 INFO @ Tue, 02 Aug 2022 15:54:23: 8000000 INFO @ Tue, 02 Aug 2022 15:54:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.05_summits.bed INFO @ Tue, 02 Aug 2022 15:54:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2106 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:54:29: 13000000 INFO @ Tue, 02 Aug 2022 15:54:30: 9000000 INFO @ Tue, 02 Aug 2022 15:54:36: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:54:36: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:54:36: #1 total tags in treatment: 5656915 INFO @ Tue, 02 Aug 2022 15:54:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:54:36: #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 15:54:36: #1 tags after filtering in treatment: 5445877 INFO @ Tue, 02 Aug 2022 15:54:36: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:54:36: #1 finished! INFO @ Tue, 02 Aug 2022 15:54:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:54:37: #2 number of paired peaks: 346 WARNING @ Tue, 02 Aug 2022 15:54:37: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 02 Aug 2022 15:54:37: start model_add_line... INFO @ Tue, 02 Aug 2022 15:54:37: start X-correlation... INFO @ Tue, 02 Aug 2022 15:54:37: end of X-cor INFO @ Tue, 02 Aug 2022 15:54:37: #2 finished! INFO @ Tue, 02 Aug 2022 15:54:37: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 15:54:37: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 15:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.10_model.r WARNING @ Tue, 02 Aug 2022 15:54:37: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:54:37: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Tue, 02 Aug 2022 15:54:37: #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 15:54:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:54:37: 10000000 INFO @ Tue, 02 Aug 2022 15:54:44: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:54:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:51: 12000000 INFO @ Tue, 02 Aug 2022 15:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.10_summits.bed INFO @ Tue, 02 Aug 2022 15:54:55: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (925 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:54:59: 13000000 INFO @ Tue, 02 Aug 2022 15:55:05: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:55:05: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:55:05: #1 total tags in treatment: 5656915 INFO @ Tue, 02 Aug 2022 15:55:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:55:05: #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 15:55:05: #1 tags after filtering in treatment: 5445877 INFO @ Tue, 02 Aug 2022 15:55:05: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:55:05: #1 finished! INFO @ Tue, 02 Aug 2022 15:55:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:55:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:55:05: #2 number of paired peaks: 346 WARNING @ Tue, 02 Aug 2022 15:55:05: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 02 Aug 2022 15:55:05: start model_add_line... INFO @ Tue, 02 Aug 2022 15:55:05: start X-correlation... INFO @ Tue, 02 Aug 2022 15:55:05: end of X-cor INFO @ Tue, 02 Aug 2022 15:55:05: #2 finished! INFO @ Tue, 02 Aug 2022 15:55:05: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 15:55:05: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 15:55:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.20_model.r WARNING @ Tue, 02 Aug 2022 15:55:05: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:55:05: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Tue, 02 Aug 2022 15:55:05: #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 15:55:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:55:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:55:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245072/SRX11245072.20_summits.bed INFO @ Tue, 02 Aug 2022 15:55:23: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (471 records, 4 fields): 54 millis CompletedMACS2peakCalling