Job ID = 14168378 SRX = SRX9263550 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18350192 spots for SRR12794430/SRR12794430.sra Written 18350192 spots for SRR12794430/SRR12794430.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169638 ("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: 00:38:11 18350192 reads; of these: 18350192 (100.00%) were paired; of these: 11491490 (62.62%) aligned concordantly 0 times 3318952 (18.09%) aligned concordantly exactly 1 time 3539750 (19.29%) aligned concordantly >1 times ---- 11491490 pairs aligned concordantly 0 times; of these: 1303515 (11.34%) aligned discordantly 1 time ---- 10187975 pairs aligned 0 times concordantly or discordantly; of these: 20375950 mates make up the pairs; of these: 17684194 (86.79%) aligned 0 times 374535 (1.84%) aligned exactly 1 time 2317221 (11.37%) aligned >1 times 51.81% overall alignment rate Time searching: 00:38:11 Overall time: 00:38:11 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] 3113055 / 8096400 = 0.3845 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 19:03:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.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 @ Fri, 10 Dec 2021 19:03:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:03:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:03:14: 1000000 INFO @ Fri, 10 Dec 2021 19:03:25: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 19:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.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 @ Fri, 10 Dec 2021 19:03:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:03:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:03:36: 3000000 INFO @ Fri, 10 Dec 2021 19:03:44: 1000000 INFO @ Fri, 10 Dec 2021 19:03:49: 4000000 INFO @ Fri, 10 Dec 2021 19:03:54: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 19:04:01: 5000000 INFO @ Fri, 10 Dec 2021 19:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.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 @ Fri, 10 Dec 2021 19:04:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:04:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:04:05: 3000000 INFO @ Fri, 10 Dec 2021 19:04:14: 6000000 INFO @ Fri, 10 Dec 2021 19:04:14: 1000000 INFO @ Fri, 10 Dec 2021 19:04:16: 4000000 INFO @ Fri, 10 Dec 2021 19:04:25: 2000000 INFO @ Fri, 10 Dec 2021 19:04:26: 7000000 INFO @ Fri, 10 Dec 2021 19:04:27: 5000000 INFO @ Fri, 10 Dec 2021 19:04:36: 3000000 INFO @ Fri, 10 Dec 2021 19:04:38: 6000000 INFO @ Fri, 10 Dec 2021 19:04:38: 8000000 INFO @ Fri, 10 Dec 2021 19:04:47: 4000000 INFO @ Fri, 10 Dec 2021 19:04:49: 7000000 INFO @ Fri, 10 Dec 2021 19:04:50: 9000000 INFO @ Fri, 10 Dec 2021 19:04:58: 5000000 INFO @ Fri, 10 Dec 2021 19:04:59: 8000000 INFO @ Fri, 10 Dec 2021 19:05:02: 10000000 INFO @ Fri, 10 Dec 2021 19:05:08: 6000000 INFO @ Fri, 10 Dec 2021 19:05:10: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:05:15: 11000000 INFO @ Fri, 10 Dec 2021 19:05:19: 7000000 INFO @ Fri, 10 Dec 2021 19:05:20: 10000000 INFO @ Fri, 10 Dec 2021 19:05:27: 12000000 INFO @ Fri, 10 Dec 2021 19:05:30: 8000000 INFO @ Fri, 10 Dec 2021 19:05:31: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:05:36: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 19:05:36: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 19:05:36: #1 total tags in treatment: 3991860 INFO @ Fri, 10 Dec 2021 19:05:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:05:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:05:36: #1 tags after filtering in treatment: 2995400 INFO @ Fri, 10 Dec 2021 19:05:36: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 19:05:36: #1 finished! INFO @ Fri, 10 Dec 2021 19:05:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:05:37: #2 number of paired peaks: 2904 INFO @ Fri, 10 Dec 2021 19:05:37: start model_add_line... INFO @ Fri, 10 Dec 2021 19:05:37: start X-correlation... INFO @ Fri, 10 Dec 2021 19:05:37: end of X-cor INFO @ Fri, 10 Dec 2021 19:05:37: #2 finished! INFO @ Fri, 10 Dec 2021 19:05:37: #2 predicted fragment length is 204 bps INFO @ Fri, 10 Dec 2021 19:05:37: #2 alternative fragment length(s) may be 204 bps INFO @ Fri, 10 Dec 2021 19:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.05_model.r WARNING @ Fri, 10 Dec 2021 19:05:37: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:05:37: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Fri, 10 Dec 2021 19:05:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:05:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:05:40: 9000000 INFO @ Fri, 10 Dec 2021 19:05:42: 12000000 INFO @ Fri, 10 Dec 2021 19:05:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.05_summits.bed INFO @ Fri, 10 Dec 2021 19:05:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4275 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:05:50: 10000000 INFO @ Fri, 10 Dec 2021 19:05:50: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 19:05:50: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 19:05:50: #1 total tags in treatment: 3991860 INFO @ Fri, 10 Dec 2021 19:05:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:05:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:05:50: #1 tags after filtering in treatment: 2995400 INFO @ Fri, 10 Dec 2021 19:05:50: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 19:05:50: #1 finished! INFO @ Fri, 10 Dec 2021 19:05:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:05:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:05:50: #2 number of paired peaks: 2904 INFO @ Fri, 10 Dec 2021 19:05:50: start model_add_line... INFO @ Fri, 10 Dec 2021 19:05:50: start X-correlation... INFO @ Fri, 10 Dec 2021 19:05:50: end of X-cor INFO @ Fri, 10 Dec 2021 19:05:50: #2 finished! INFO @ Fri, 10 Dec 2021 19:05:50: #2 predicted fragment length is 204 bps INFO @ Fri, 10 Dec 2021 19:05:50: #2 alternative fragment length(s) may be 204 bps INFO @ Fri, 10 Dec 2021 19:05:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.10_model.r WARNING @ Fri, 10 Dec 2021 19:05:50: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:05:50: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Fri, 10 Dec 2021 19:05:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:05:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:05:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:05:59: 11000000 INFO @ Fri, 10 Dec 2021 19:06:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:06:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:06:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.10_summits.bed INFO @ Fri, 10 Dec 2021 19:06:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1900 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:06:08: 12000000 INFO @ Fri, 10 Dec 2021 19:06:15: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 19:06:15: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 19:06:15: #1 total tags in treatment: 3991860 INFO @ Fri, 10 Dec 2021 19:06:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:06:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 19:06:15: #1 tags after filtering in treatment: 2995400 INFO @ Fri, 10 Dec 2021 19:06:15: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 19:06:15: #1 finished! INFO @ Fri, 10 Dec 2021 19:06:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:06:15: #2 number of paired peaks: 2904 INFO @ Fri, 10 Dec 2021 19:06:15: start model_add_line... INFO @ Fri, 10 Dec 2021 19:06:15: start X-correlation... INFO @ Fri, 10 Dec 2021 19:06:15: end of X-cor INFO @ Fri, 10 Dec 2021 19:06:15: #2 finished! INFO @ Fri, 10 Dec 2021 19:06:15: #2 predicted fragment length is 204 bps INFO @ Fri, 10 Dec 2021 19:06:15: #2 alternative fragment length(s) may be 204 bps INFO @ Fri, 10 Dec 2021 19:06:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.20_model.r WARNING @ Fri, 10 Dec 2021 19:06:15: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:06:15: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Fri, 10 Dec 2021 19:06:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 19:06:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:06:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:06:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:06:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:06:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:06:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263550/SRX9263550.20_summits.bed INFO @ Fri, 10 Dec 2021 19:06:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling