Job ID = 14170122 SRX = SRX8556379 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29757885 spots for SRR12024935/SRR12024935.sra Written 29757885 spots for SRR12024935/SRR12024935.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170712 ("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: 00:19:48 29757885 reads; of these: 29757885 (100.00%) were paired; of these: 27321894 (91.81%) aligned concordantly 0 times 1758176 (5.91%) aligned concordantly exactly 1 time 677815 (2.28%) aligned concordantly >1 times ---- 27321894 pairs aligned concordantly 0 times; of these: 201045 (0.74%) aligned discordantly 1 time ---- 27120849 pairs aligned 0 times concordantly or discordantly; of these: 54241698 mates make up the pairs; of these: 53396332 (98.44%) aligned 0 times 497861 (0.92%) aligned exactly 1 time 347505 (0.64%) aligned >1 times 10.28% overall alignment rate Time searching: 00:19:49 Overall time: 00:19:49 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 8 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] 1890693 / 2608086 = 0.7249 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 @ Sat, 11 Dec 2021 06:06:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.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 @ Sat, 11 Dec 2021 06:06:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:06:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:06:15: 1000000 INFO @ Sat, 11 Dec 2021 06:06:25: 2000000 INFO @ Sat, 11 Dec 2021 06:06:28: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:06:28: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:06:28: #1 total tags in treatment: 646565 INFO @ Sat, 11 Dec 2021 06:06:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:06:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:06:28: #1 tags after filtering in treatment: 556463 INFO @ Sat, 11 Dec 2021 06:06:28: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 06:06:28: #1 finished! INFO @ Sat, 11 Dec 2021 06:06:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:06:29: #2 number of paired peaks: 2604 INFO @ Sat, 11 Dec 2021 06:06:29: start model_add_line... INFO @ Sat, 11 Dec 2021 06:06:29: start X-correlation... INFO @ Sat, 11 Dec 2021 06:06:29: end of X-cor INFO @ Sat, 11 Dec 2021 06:06:29: #2 finished! INFO @ Sat, 11 Dec 2021 06:06:29: #2 predicted fragment length is 171 bps INFO @ Sat, 11 Dec 2021 06:06:29: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 11 Dec 2021 06:06:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.05_model.r WARNING @ Sat, 11 Dec 2021 06:06:29: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:06:29: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Sat, 11 Dec 2021 06:06:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:06:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:06:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:06:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:06:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.05_summits.bed INFO @ Sat, 11 Dec 2021 06:06:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 06:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.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 @ Sat, 11 Dec 2021 06:06:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:06:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:06:45: 1000000 INFO @ Sat, 11 Dec 2021 06:06:55: 2000000 INFO @ Sat, 11 Dec 2021 06:06:58: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:06:58: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:06:58: #1 total tags in treatment: 646565 INFO @ Sat, 11 Dec 2021 06:06:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:06:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:06:58: #1 tags after filtering in treatment: 556463 INFO @ Sat, 11 Dec 2021 06:06:58: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 06:06:58: #1 finished! INFO @ Sat, 11 Dec 2021 06:06:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:06:58: #2 number of paired peaks: 2604 INFO @ Sat, 11 Dec 2021 06:06:58: start model_add_line... INFO @ Sat, 11 Dec 2021 06:06:58: start X-correlation... INFO @ Sat, 11 Dec 2021 06:06:58: end of X-cor INFO @ Sat, 11 Dec 2021 06:06:58: #2 finished! INFO @ Sat, 11 Dec 2021 06:06:58: #2 predicted fragment length is 171 bps INFO @ Sat, 11 Dec 2021 06:06:58: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 11 Dec 2021 06:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.10_model.r WARNING @ Sat, 11 Dec 2021 06:06:58: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:06:58: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Sat, 11 Dec 2021 06:06:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:06:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:07:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:07:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:07:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:07:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.10_summits.bed INFO @ Sat, 11 Dec 2021 06:07:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 06:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.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 @ Sat, 11 Dec 2021 06:07:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:07:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:07:16: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:07:26: 2000000 INFO @ Sat, 11 Dec 2021 06:07:29: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:07:29: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:07:29: #1 total tags in treatment: 646565 INFO @ Sat, 11 Dec 2021 06:07:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:07:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:07:29: #1 tags after filtering in treatment: 556463 INFO @ Sat, 11 Dec 2021 06:07:29: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 06:07:29: #1 finished! INFO @ Sat, 11 Dec 2021 06:07:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:07:29: #2 number of paired peaks: 2604 INFO @ Sat, 11 Dec 2021 06:07:29: start model_add_line... INFO @ Sat, 11 Dec 2021 06:07:29: start X-correlation... INFO @ Sat, 11 Dec 2021 06:07:29: end of X-cor INFO @ Sat, 11 Dec 2021 06:07:29: #2 finished! INFO @ Sat, 11 Dec 2021 06:07:29: #2 predicted fragment length is 171 bps INFO @ Sat, 11 Dec 2021 06:07:29: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 11 Dec 2021 06:07:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.20_model.r WARNING @ Sat, 11 Dec 2021 06:07:29: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:07:29: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Sat, 11 Dec 2021 06:07:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:07:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:07:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556379/SRX8556379.20_summits.bed INFO @ Sat, 11 Dec 2021 06:07:31: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (289 records, 4 fields): 2 millis CompletedMACS2peakCalling