Job ID = 14168368 SRX = SRX8556400 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17168677 spots for SRR12024956/SRR12024956.sra Written 17168677 spots for SRR12024956/SRR12024956.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169580 ("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: 00:16:36 17168677 reads; of these: 17168677 (100.00%) were paired; of these: 14991329 (87.32%) aligned concordantly 0 times 1496046 (8.71%) aligned concordantly exactly 1 time 681302 (3.97%) aligned concordantly >1 times ---- 14991329 pairs aligned concordantly 0 times; of these: 334151 (2.23%) aligned discordantly 1 time ---- 14657178 pairs aligned 0 times concordantly or discordantly; of these: 29314356 mates make up the pairs; of these: 28433835 (97.00%) aligned 0 times 463328 (1.58%) aligned exactly 1 time 417193 (1.42%) aligned >1 times 17.19% overall alignment rate Time searching: 00:16:36 Overall time: 00:16:36 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] 1673444 / 2467717 = 0.6781 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 18:32:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.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 18:32:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:32:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:32:32: 1000000 INFO @ Fri, 10 Dec 2021 18:32:39: 2000000 INFO @ Fri, 10 Dec 2021 18:32:42: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 18:32:42: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 18:32:42: #1 total tags in treatment: 681993 INFO @ Fri, 10 Dec 2021 18:32:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:32:42: #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 18:32:42: #1 tags after filtering in treatment: 567127 INFO @ Fri, 10 Dec 2021 18:32:42: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Dec 2021 18:32:42: #1 finished! INFO @ Fri, 10 Dec 2021 18:32:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:32:42: #2 number of paired peaks: 2720 INFO @ Fri, 10 Dec 2021 18:32:42: start model_add_line... INFO @ Fri, 10 Dec 2021 18:32:42: start X-correlation... INFO @ Fri, 10 Dec 2021 18:32:42: end of X-cor INFO @ Fri, 10 Dec 2021 18:32:42: #2 finished! INFO @ Fri, 10 Dec 2021 18:32:42: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 18:32:42: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 18:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.05_model.r WARNING @ Fri, 10 Dec 2021 18:32:42: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:32:42: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Fri, 10 Dec 2021 18:32:42: #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 18:32:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:32:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.05_summits.bed INFO @ Fri, 10 Dec 2021 18:32:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1343 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 @ Fri, 10 Dec 2021 18:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.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 18:32:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:32:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:33:02: 1000000 INFO @ Fri, 10 Dec 2021 18:33:09: 2000000 INFO @ Fri, 10 Dec 2021 18:33:12: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 18:33:12: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 18:33:12: #1 total tags in treatment: 681993 INFO @ Fri, 10 Dec 2021 18:33:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:33:12: #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 18:33:12: #1 tags after filtering in treatment: 567127 INFO @ Fri, 10 Dec 2021 18:33:12: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Dec 2021 18:33:12: #1 finished! INFO @ Fri, 10 Dec 2021 18:33:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:33:12: #2 number of paired peaks: 2720 INFO @ Fri, 10 Dec 2021 18:33:12: start model_add_line... INFO @ Fri, 10 Dec 2021 18:33:12: start X-correlation... INFO @ Fri, 10 Dec 2021 18:33:12: end of X-cor INFO @ Fri, 10 Dec 2021 18:33:12: #2 finished! INFO @ Fri, 10 Dec 2021 18:33:12: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 18:33:12: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 18:33:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.10_model.r WARNING @ Fri, 10 Dec 2021 18:33:12: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:33:12: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Fri, 10 Dec 2021 18:33:12: #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 18:33:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:33:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:33:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:33:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:33:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:33:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.10_summits.bed INFO @ Fri, 10 Dec 2021 18:33:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 2 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 @ Fri, 10 Dec 2021 18:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.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 18:33:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:33:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:33:33: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:33:41: 2000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:33:46: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 18:33:46: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 18:33:46: #1 total tags in treatment: 681993 INFO @ Fri, 10 Dec 2021 18:33:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:33:46: #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 18:33:46: #1 tags after filtering in treatment: 567127 INFO @ Fri, 10 Dec 2021 18:33:46: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Dec 2021 18:33:46: #1 finished! INFO @ Fri, 10 Dec 2021 18:33:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:33:46: #2 number of paired peaks: 2720 INFO @ Fri, 10 Dec 2021 18:33:46: start model_add_line... INFO @ Fri, 10 Dec 2021 18:33:46: start X-correlation... INFO @ Fri, 10 Dec 2021 18:33:46: end of X-cor INFO @ Fri, 10 Dec 2021 18:33:46: #2 finished! INFO @ Fri, 10 Dec 2021 18:33:46: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 18:33:46: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 18:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.20_model.r WARNING @ Fri, 10 Dec 2021 18:33:46: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:33:46: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Fri, 10 Dec 2021 18:33:46: #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 18:33:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:33:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:33:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:33:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:33:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556400/SRX8556400.20_summits.bed INFO @ Fri, 10 Dec 2021 18:33:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 2 millis CompletedMACS2peakCalling