Job ID = 16439987 SRX = SRX12175824 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23763961 spots for SRR15884963/SRR15884963.sra Written 23763961 spots for SRR15884963/SRR15884963.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440730 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:10:17 23763961 reads; of these: 23763961 (100.00%) were paired; of these: 13814144 (58.13%) aligned concordantly 0 times 8221816 (34.60%) aligned concordantly exactly 1 time 1728001 (7.27%) aligned concordantly >1 times ---- 13814144 pairs aligned concordantly 0 times; of these: 2982919 (21.59%) aligned discordantly 1 time ---- 10831225 pairs aligned 0 times concordantly or discordantly; of these: 21662450 mates make up the pairs; of these: 19843420 (91.60%) aligned 0 times 798863 (3.69%) aligned exactly 1 time 1020167 (4.71%) aligned >1 times 58.25% overall alignment rate Time searching: 01:10:18 Overall time: 01:10:18 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 24 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] 1888424 / 12877586 = 0.1466 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 18:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.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 18:01:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:01:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:01:28: 1000000 INFO @ Tue, 02 Aug 2022 18:01:40: 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 18:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.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 18:01:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:01:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:01:53: 3000000 INFO @ Tue, 02 Aug 2022 18:01:55: 1000000 INFO @ Tue, 02 Aug 2022 18:02:05: 4000000 INFO @ Tue, 02 Aug 2022 18:02:06: 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 18:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.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 18:02:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:02:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:02:17: 3000000 INFO @ Tue, 02 Aug 2022 18:02:18: 5000000 INFO @ Tue, 02 Aug 2022 18:02:28: 4000000 INFO @ Tue, 02 Aug 2022 18:02:30: 1000000 INFO @ Tue, 02 Aug 2022 18:02:32: 6000000 INFO @ Tue, 02 Aug 2022 18:02:41: 5000000 INFO @ Tue, 02 Aug 2022 18:02:45: 2000000 INFO @ Tue, 02 Aug 2022 18:02:47: 7000000 INFO @ Tue, 02 Aug 2022 18:02:53: 6000000 INFO @ Tue, 02 Aug 2022 18:02:59: 3000000 INFO @ Tue, 02 Aug 2022 18:03:02: 8000000 INFO @ Tue, 02 Aug 2022 18:03:05: 7000000 INFO @ Tue, 02 Aug 2022 18:03:13: 4000000 INFO @ Tue, 02 Aug 2022 18:03:16: 9000000 INFO @ Tue, 02 Aug 2022 18:03:17: 8000000 INFO @ Tue, 02 Aug 2022 18:03:27: 5000000 INFO @ Tue, 02 Aug 2022 18:03:29: 9000000 INFO @ Tue, 02 Aug 2022 18:03:30: 10000000 INFO @ Tue, 02 Aug 2022 18:03:41: 6000000 INFO @ Tue, 02 Aug 2022 18:03:41: 10000000 INFO @ Tue, 02 Aug 2022 18:03:43: 11000000 INFO @ Tue, 02 Aug 2022 18:03:53: 11000000 INFO @ Tue, 02 Aug 2022 18:03:55: 7000000 INFO @ Tue, 02 Aug 2022 18:03:57: 12000000 INFO @ Tue, 02 Aug 2022 18:04:05: 12000000 INFO @ Tue, 02 Aug 2022 18:04:09: 8000000 INFO @ Tue, 02 Aug 2022 18:04:12: 13000000 INFO @ Tue, 02 Aug 2022 18:04:16: 13000000 INFO @ Tue, 02 Aug 2022 18:04:23: 9000000 INFO @ Tue, 02 Aug 2022 18:04:26: 14000000 INFO @ Tue, 02 Aug 2022 18:04:29: 14000000 INFO @ Tue, 02 Aug 2022 18:04:37: 10000000 INFO @ Tue, 02 Aug 2022 18:04:40: 15000000 INFO @ Tue, 02 Aug 2022 18:04:41: 15000000 INFO @ Tue, 02 Aug 2022 18:04:51: 11000000 INFO @ Tue, 02 Aug 2022 18:04:53: 16000000 INFO @ Tue, 02 Aug 2022 18:04:53: 16000000 INFO @ Tue, 02 Aug 2022 18:05:05: 12000000 INFO @ Tue, 02 Aug 2022 18:05:05: 17000000 INFO @ Tue, 02 Aug 2022 18:05:06: 17000000 INFO @ Tue, 02 Aug 2022 18:05:18: 18000000 INFO @ Tue, 02 Aug 2022 18:05:19: 18000000 INFO @ Tue, 02 Aug 2022 18:05:22: 13000000 INFO @ Tue, 02 Aug 2022 18:05:31: 19000000 INFO @ Tue, 02 Aug 2022 18:05:32: 19000000 INFO @ Tue, 02 Aug 2022 18:05:38: 14000000 INFO @ Tue, 02 Aug 2022 18:05:44: 20000000 INFO @ Tue, 02 Aug 2022 18:05:45: 20000000 INFO @ Tue, 02 Aug 2022 18:05:55: 15000000 INFO @ Tue, 02 Aug 2022 18:05:57: 21000000 INFO @ Tue, 02 Aug 2022 18:05:58: 21000000 INFO @ Tue, 02 Aug 2022 18:06:09: 22000000 INFO @ Tue, 02 Aug 2022 18:06:10: 16000000 INFO @ Tue, 02 Aug 2022 18:06:11: 22000000 INFO @ Tue, 02 Aug 2022 18:06:22: 23000000 INFO @ Tue, 02 Aug 2022 18:06:24: 17000000 INFO @ Tue, 02 Aug 2022 18:06:25: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:06:32: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:06:32: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:06:32: #1 total tags in treatment: 8387048 INFO @ Tue, 02 Aug 2022 18:06:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:06:32: #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 18:06:33: #1 tags after filtering in treatment: 6000150 INFO @ Tue, 02 Aug 2022 18:06:33: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 18:06:33: #1 finished! INFO @ Tue, 02 Aug 2022 18:06:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:06:33: #2 number of paired peaks: 3739 INFO @ Tue, 02 Aug 2022 18:06:33: start model_add_line... INFO @ Tue, 02 Aug 2022 18:06:33: start X-correlation... INFO @ Tue, 02 Aug 2022 18:06:34: end of X-cor INFO @ Tue, 02 Aug 2022 18:06:34: #2 finished! INFO @ Tue, 02 Aug 2022 18:06:34: #2 predicted fragment length is 255 bps INFO @ Tue, 02 Aug 2022 18:06:34: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 02 Aug 2022 18:06:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.10_model.r WARNING @ Tue, 02 Aug 2022 18:06:34: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:06:34: #2 You may need to consider one of the other alternative d(s): 255 WARNING @ Tue, 02 Aug 2022 18:06:34: #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 18:06:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:06:37: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:06:37: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:06:37: #1 total tags in treatment: 8387048 INFO @ Tue, 02 Aug 2022 18:06:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:06:37: #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 18:06:38: #1 tags after filtering in treatment: 6000150 INFO @ Tue, 02 Aug 2022 18:06:38: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 18:06:38: #1 finished! INFO @ Tue, 02 Aug 2022 18:06:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:06:38: 18000000 INFO @ Tue, 02 Aug 2022 18:06:38: #2 number of paired peaks: 3739 INFO @ Tue, 02 Aug 2022 18:06:38: start model_add_line... INFO @ Tue, 02 Aug 2022 18:06:38: start X-correlation... INFO @ Tue, 02 Aug 2022 18:06:38: end of X-cor INFO @ Tue, 02 Aug 2022 18:06:38: #2 finished! INFO @ Tue, 02 Aug 2022 18:06:38: #2 predicted fragment length is 255 bps INFO @ Tue, 02 Aug 2022 18:06:38: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 02 Aug 2022 18:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.05_model.r WARNING @ Tue, 02 Aug 2022 18:06:38: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:06:38: #2 You may need to consider one of the other alternative d(s): 255 WARNING @ Tue, 02 Aug 2022 18:06:38: #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 18:06:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:06:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:06:50: 19000000 INFO @ Tue, 02 Aug 2022 18:06:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.10_summits.bed INFO @ Tue, 02 Aug 2022 18:06:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5610 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:07:02: 20000000 INFO @ Tue, 02 Aug 2022 18:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.05_summits.bed INFO @ Tue, 02 Aug 2022 18:07:02: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8371 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:07:13: 21000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:07:24: 22000000 INFO @ Tue, 02 Aug 2022 18:07:35: 23000000 INFO @ Tue, 02 Aug 2022 18:07:45: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:07:45: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:07:45: #1 total tags in treatment: 8387048 INFO @ Tue, 02 Aug 2022 18:07:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:07:45: #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 18:07:45: #1 tags after filtering in treatment: 6000150 INFO @ Tue, 02 Aug 2022 18:07:45: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 18:07:45: #1 finished! INFO @ Tue, 02 Aug 2022 18:07:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:07:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:07:46: #2 number of paired peaks: 3739 INFO @ Tue, 02 Aug 2022 18:07:46: start model_add_line... INFO @ Tue, 02 Aug 2022 18:07:46: start X-correlation... INFO @ Tue, 02 Aug 2022 18:07:46: end of X-cor INFO @ Tue, 02 Aug 2022 18:07:46: #2 finished! INFO @ Tue, 02 Aug 2022 18:07:46: #2 predicted fragment length is 255 bps INFO @ Tue, 02 Aug 2022 18:07:46: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 02 Aug 2022 18:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.20_model.r WARNING @ Tue, 02 Aug 2022 18:07:47: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:07:47: #2 You may need to consider one of the other alternative d(s): 255 WARNING @ Tue, 02 Aug 2022 18:07:47: #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 18:07:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:07:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:08:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175824/SRX12175824.20_summits.bed INFO @ Tue, 02 Aug 2022 18:08:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2853 records, 4 fields): 24 millis CompletedMACS2peakCalling