Job ID = 16439992 SRX = SRX12175828 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27708699 spots for SRR15884967/SRR15884967.sra Written 27708699 spots for SRR15884967/SRR15884967.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440264 ("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: 00:57:54 27708699 reads; of these: 27708699 (100.00%) were paired; of these: 21018041 (75.85%) aligned concordantly 0 times 5164183 (18.64%) aligned concordantly exactly 1 time 1526475 (5.51%) aligned concordantly >1 times ---- 21018041 pairs aligned concordantly 0 times; of these: 1579377 (7.51%) aligned discordantly 1 time ---- 19438664 pairs aligned 0 times concordantly or discordantly; of these: 38877328 mates make up the pairs; of these: 37644923 (96.83%) aligned 0 times 455834 (1.17%) aligned exactly 1 time 776571 (2.00%) aligned >1 times 32.07% overall alignment rate Time searching: 00:57:55 Overall time: 00:57:55 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] 1192143 / 8232454 = 0.1448 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 17:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.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 17:46:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:46:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:46:24: 1000000 INFO @ Tue, 02 Aug 2022 17:46:36: 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 17:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.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 17:46:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:46:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:46:47: 3000000 INFO @ Tue, 02 Aug 2022 17:46:53: 1000000 INFO @ Tue, 02 Aug 2022 17:47:00: 4000000 INFO @ Tue, 02 Aug 2022 17:47:05: 2000000 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 17:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.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 17:47:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:47:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:47:12: 5000000 INFO @ Tue, 02 Aug 2022 17:47:17: 3000000 INFO @ Tue, 02 Aug 2022 17:47:24: 6000000 INFO @ Tue, 02 Aug 2022 17:47:24: 1000000 INFO @ Tue, 02 Aug 2022 17:47:30: 4000000 INFO @ Tue, 02 Aug 2022 17:47:37: 7000000 INFO @ Tue, 02 Aug 2022 17:47:37: 2000000 INFO @ Tue, 02 Aug 2022 17:47:42: 5000000 INFO @ Tue, 02 Aug 2022 17:47:49: 8000000 INFO @ Tue, 02 Aug 2022 17:47:50: 3000000 INFO @ Tue, 02 Aug 2022 17:47:54: 6000000 INFO @ Tue, 02 Aug 2022 17:48:01: 9000000 INFO @ Tue, 02 Aug 2022 17:48:03: 4000000 INFO @ Tue, 02 Aug 2022 17:48:06: 7000000 INFO @ Tue, 02 Aug 2022 17:48:13: 10000000 INFO @ Tue, 02 Aug 2022 17:48:15: 5000000 INFO @ Tue, 02 Aug 2022 17:48:18: 8000000 INFO @ Tue, 02 Aug 2022 17:48:26: 11000000 INFO @ Tue, 02 Aug 2022 17:48:28: 6000000 INFO @ Tue, 02 Aug 2022 17:48:30: 9000000 INFO @ Tue, 02 Aug 2022 17:48:38: 12000000 INFO @ Tue, 02 Aug 2022 17:48:41: 7000000 INFO @ Tue, 02 Aug 2022 17:48:42: 10000000 INFO @ Tue, 02 Aug 2022 17:48:50: 13000000 INFO @ Tue, 02 Aug 2022 17:48:54: 8000000 INFO @ Tue, 02 Aug 2022 17:48:54: 11000000 INFO @ Tue, 02 Aug 2022 17:49:06: 14000000 INFO @ Tue, 02 Aug 2022 17:49:06: 12000000 INFO @ Tue, 02 Aug 2022 17:49:07: 9000000 INFO @ Tue, 02 Aug 2022 17:49:18: 13000000 INFO @ Tue, 02 Aug 2022 17:49:19: 10000000 INFO @ Tue, 02 Aug 2022 17:49:21: 15000000 INFO @ Tue, 02 Aug 2022 17:49:26: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:49:26: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:49:26: #1 total tags in treatment: 5655184 INFO @ Tue, 02 Aug 2022 17:49:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:49:26: #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 17:49:26: #1 tags after filtering in treatment: 4489676 INFO @ Tue, 02 Aug 2022 17:49:26: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 17:49:26: #1 finished! INFO @ Tue, 02 Aug 2022 17:49:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:49:26: #2 number of paired peaks: 2547 INFO @ Tue, 02 Aug 2022 17:49:26: start model_add_line... INFO @ Tue, 02 Aug 2022 17:49:26: start X-correlation... INFO @ Tue, 02 Aug 2022 17:49:26: end of X-cor INFO @ Tue, 02 Aug 2022 17:49:26: #2 finished! INFO @ Tue, 02 Aug 2022 17:49:26: #2 predicted fragment length is 240 bps INFO @ Tue, 02 Aug 2022 17:49:26: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 02 Aug 2022 17:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.05_model.r WARNING @ Tue, 02 Aug 2022 17:49:26: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:49:26: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 02 Aug 2022 17:49:26: #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 17:49:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:49:31: 14000000 INFO @ Tue, 02 Aug 2022 17:49:34: 11000000 INFO @ Tue, 02 Aug 2022 17:49:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.05_summits.bed INFO @ Tue, 02 Aug 2022 17:49:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6223 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:49:44: 15000000 INFO @ Tue, 02 Aug 2022 17:49:46: 12000000 INFO @ Tue, 02 Aug 2022 17:49:49: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:49:49: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:49:49: #1 total tags in treatment: 5655184 INFO @ Tue, 02 Aug 2022 17:49:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:49:49: #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 17:49:49: #1 tags after filtering in treatment: 4489676 INFO @ Tue, 02 Aug 2022 17:49:49: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 17:49:49: #1 finished! INFO @ Tue, 02 Aug 2022 17:49:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:49:50: #2 number of paired peaks: 2547 INFO @ Tue, 02 Aug 2022 17:49:50: start model_add_line... INFO @ Tue, 02 Aug 2022 17:49:50: start X-correlation... INFO @ Tue, 02 Aug 2022 17:49:50: end of X-cor INFO @ Tue, 02 Aug 2022 17:49:50: #2 finished! INFO @ Tue, 02 Aug 2022 17:49:50: #2 predicted fragment length is 240 bps INFO @ Tue, 02 Aug 2022 17:49:50: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 02 Aug 2022 17:49:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.10_model.r WARNING @ Tue, 02 Aug 2022 17:49:50: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:49:50: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 02 Aug 2022 17:49:50: #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 17:49:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:49:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:49:59: 13000000 INFO @ Tue, 02 Aug 2022 17:50:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:50:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:50:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:50:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.10_summits.bed INFO @ Tue, 02 Aug 2022 17:50:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3649 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:50:12: 14000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:50:24: 15000000 INFO @ Tue, 02 Aug 2022 17:50:29: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:50:29: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:50:29: #1 total tags in treatment: 5655184 INFO @ Tue, 02 Aug 2022 17:50:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:50:29: #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 17:50:29: #1 tags after filtering in treatment: 4489676 INFO @ Tue, 02 Aug 2022 17:50:29: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 17:50:29: #1 finished! INFO @ Tue, 02 Aug 2022 17:50:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:50:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:50:30: #2 number of paired peaks: 2547 INFO @ Tue, 02 Aug 2022 17:50:30: start model_add_line... INFO @ Tue, 02 Aug 2022 17:50:30: start X-correlation... INFO @ Tue, 02 Aug 2022 17:50:30: end of X-cor INFO @ Tue, 02 Aug 2022 17:50:30: #2 finished! INFO @ Tue, 02 Aug 2022 17:50:30: #2 predicted fragment length is 240 bps INFO @ Tue, 02 Aug 2022 17:50:30: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 02 Aug 2022 17:50:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.20_model.r WARNING @ Tue, 02 Aug 2022 17:50:30: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:50:30: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 02 Aug 2022 17:50:30: #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 17:50:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:50:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:50:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:50:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:50:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:50:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175828/SRX12175828.20_summits.bed INFO @ Tue, 02 Aug 2022 17:50:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1622 records, 4 fields): 28 millis CompletedMACS2peakCalling