Job ID = 16437211 SRX = SRX12119059 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36922417 spots for SRR15827097/SRR15827097.sra Written 36922417 spots for SRR15827097/SRR15827097.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438034 ("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: 00:48:43 36922417 reads; of these: 36922417 (100.00%) were paired; of these: 29009465 (78.57%) aligned concordantly 0 times 5886076 (15.94%) aligned concordantly exactly 1 time 2026876 (5.49%) aligned concordantly >1 times ---- 29009465 pairs aligned concordantly 0 times; of these: 2069330 (7.13%) aligned discordantly 1 time ---- 26940135 pairs aligned 0 times concordantly or discordantly; of these: 53880270 mates make up the pairs; of these: 51579472 (95.73%) aligned 0 times 1016104 (1.89%) aligned exactly 1 time 1284694 (2.38%) aligned >1 times 30.15% overall alignment rate Time searching: 00:48:43 Overall time: 00:48:43 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 20 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] 1676908 / 9928038 = 0.1689 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 13:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.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 13:24:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:24:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:24:32: 1000000 INFO @ Tue, 02 Aug 2022 13:24:42: 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 13:24:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.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 13:24:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:24:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:24:52: 3000000 INFO @ Tue, 02 Aug 2022 13:25:02: 1000000 INFO @ Tue, 02 Aug 2022 13:25:03: 4000000 INFO @ Tue, 02 Aug 2022 13:25:13: 2000000 INFO @ Tue, 02 Aug 2022 13:25:15: 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 13:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.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 13:25:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:25:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:25:23: 3000000 INFO @ Tue, 02 Aug 2022 13:25:25: 6000000 INFO @ Tue, 02 Aug 2022 13:25:32: 1000000 INFO @ Tue, 02 Aug 2022 13:25:34: 4000000 INFO @ Tue, 02 Aug 2022 13:25:37: 7000000 INFO @ Tue, 02 Aug 2022 13:25:42: 2000000 INFO @ Tue, 02 Aug 2022 13:25:45: 5000000 INFO @ Tue, 02 Aug 2022 13:25:48: 8000000 INFO @ Tue, 02 Aug 2022 13:25:53: 3000000 INFO @ Tue, 02 Aug 2022 13:25:55: 6000000 INFO @ Tue, 02 Aug 2022 13:25:59: 9000000 INFO @ Tue, 02 Aug 2022 13:26:03: 4000000 INFO @ Tue, 02 Aug 2022 13:26:06: 7000000 INFO @ Tue, 02 Aug 2022 13:26:10: 10000000 INFO @ Tue, 02 Aug 2022 13:26:14: 5000000 INFO @ Tue, 02 Aug 2022 13:26:16: 8000000 INFO @ Tue, 02 Aug 2022 13:26:21: 11000000 INFO @ Tue, 02 Aug 2022 13:26:24: 6000000 INFO @ Tue, 02 Aug 2022 13:26:26: 9000000 INFO @ Tue, 02 Aug 2022 13:26:33: 12000000 INFO @ Tue, 02 Aug 2022 13:26:34: 7000000 INFO @ Tue, 02 Aug 2022 13:26:36: 10000000 INFO @ Tue, 02 Aug 2022 13:26:44: 13000000 INFO @ Tue, 02 Aug 2022 13:26:44: 8000000 INFO @ Tue, 02 Aug 2022 13:26:47: 11000000 INFO @ Tue, 02 Aug 2022 13:26:55: 9000000 INFO @ Tue, 02 Aug 2022 13:26:55: 14000000 INFO @ Tue, 02 Aug 2022 13:26:58: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:27:05: 10000000 INFO @ Tue, 02 Aug 2022 13:27:07: 15000000 INFO @ Tue, 02 Aug 2022 13:27:10: 13000000 INFO @ Tue, 02 Aug 2022 13:27:15: 11000000 INFO @ Tue, 02 Aug 2022 13:27:19: 16000000 INFO @ Tue, 02 Aug 2022 13:27:21: 14000000 INFO @ Tue, 02 Aug 2022 13:27:27: 12000000 INFO @ Tue, 02 Aug 2022 13:27:30: 17000000 INFO @ Tue, 02 Aug 2022 13:27:33: 15000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:27:38: 13000000 INFO @ Tue, 02 Aug 2022 13:27:42: 18000000 INFO @ Tue, 02 Aug 2022 13:27:44: 16000000 INFO @ Tue, 02 Aug 2022 13:27:49: 14000000 INFO @ Tue, 02 Aug 2022 13:27:52: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:27:52: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:27:52: #1 total tags in treatment: 6488625 INFO @ Tue, 02 Aug 2022 13:27:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:27:52: #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 13:27:52: #1 tags after filtering in treatment: 5074601 INFO @ Tue, 02 Aug 2022 13:27:52: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 13:27:52: #1 finished! INFO @ Tue, 02 Aug 2022 13:27:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:27:53: #2 number of paired peaks: 2858 INFO @ Tue, 02 Aug 2022 13:27:53: start model_add_line... INFO @ Tue, 02 Aug 2022 13:27:53: start X-correlation... INFO @ Tue, 02 Aug 2022 13:27:53: end of X-cor INFO @ Tue, 02 Aug 2022 13:27:53: #2 finished! INFO @ Tue, 02 Aug 2022 13:27:53: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 13:27:53: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 02 Aug 2022 13:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.05_model.r WARNING @ Tue, 02 Aug 2022 13:27:53: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:27:53: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 02 Aug 2022 13:27:53: #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 13:27:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:27:56: 17000000 INFO @ Tue, 02 Aug 2022 13:28:00: 15000000 INFO @ Tue, 02 Aug 2022 13:28:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:28:07: 18000000 INFO @ Tue, 02 Aug 2022 13:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:28:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.05_summits.bed INFO @ Tue, 02 Aug 2022 13:28:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7466 records, 4 fields): 88 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:28:11: 16000000 INFO @ Tue, 02 Aug 2022 13:28:17: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:28:17: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:28:17: #1 total tags in treatment: 6488625 INFO @ Tue, 02 Aug 2022 13:28:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:28:17: #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 13:28:17: #1 tags after filtering in treatment: 5074601 INFO @ Tue, 02 Aug 2022 13:28:17: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 13:28:17: #1 finished! INFO @ Tue, 02 Aug 2022 13:28:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:28:17: #2 number of paired peaks: 2858 INFO @ Tue, 02 Aug 2022 13:28:17: start model_add_line... INFO @ Tue, 02 Aug 2022 13:28:17: start X-correlation... INFO @ Tue, 02 Aug 2022 13:28:17: end of X-cor INFO @ Tue, 02 Aug 2022 13:28:17: #2 finished! INFO @ Tue, 02 Aug 2022 13:28:17: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 13:28:17: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 02 Aug 2022 13:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.10_model.r WARNING @ Tue, 02 Aug 2022 13:28:18: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:28:18: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 02 Aug 2022 13:28:18: #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 13:28:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:28:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:28:22: 17000000 INFO @ Tue, 02 Aug 2022 13:28:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:28:33: 18000000 INFO @ Tue, 02 Aug 2022 13:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.10_summits.bed INFO @ Tue, 02 Aug 2022 13:28:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4620 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:28:42: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:28:42: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:28:42: #1 total tags in treatment: 6488625 INFO @ Tue, 02 Aug 2022 13:28:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:28:42: #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 13:28:42: #1 tags after filtering in treatment: 5074601 INFO @ Tue, 02 Aug 2022 13:28:42: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 13:28:42: #1 finished! INFO @ Tue, 02 Aug 2022 13:28:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:28:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:28:42: #2 number of paired peaks: 2858 INFO @ Tue, 02 Aug 2022 13:28:42: start model_add_line... INFO @ Tue, 02 Aug 2022 13:28:42: start X-correlation... INFO @ Tue, 02 Aug 2022 13:28:43: end of X-cor INFO @ Tue, 02 Aug 2022 13:28:43: #2 finished! INFO @ Tue, 02 Aug 2022 13:28:43: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 13:28:43: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 02 Aug 2022 13:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.20_model.r WARNING @ Tue, 02 Aug 2022 13:28:43: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:28:43: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 02 Aug 2022 13:28:43: #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 13:28:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:28:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119059/SRX12119059.20_summits.bed INFO @ Tue, 02 Aug 2022 13:29:01: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2015 records, 4 fields): 21 millis CompletedMACS2peakCalling