Job ID = 14170268 SRX = SRX8556390 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29726213 spots for SRR12024946/SRR12024946.sra Written 29726213 spots for SRR12024946/SRR12024946.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170734 ("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: 00:14:05 29726213 reads; of these: 29726213 (100.00%) were paired; of these: 29103314 (97.90%) aligned concordantly 0 times 424829 (1.43%) aligned concordantly exactly 1 time 198070 (0.67%) aligned concordantly >1 times ---- 29103314 pairs aligned concordantly 0 times; of these: 89366 (0.31%) aligned discordantly 1 time ---- 29013948 pairs aligned 0 times concordantly or discordantly; of these: 58027896 mates make up the pairs; of these: 57751393 (99.52%) aligned 0 times 118368 (0.20%) aligned exactly 1 time 158135 (0.27%) aligned >1 times 2.86% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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_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] 484703 / 703244 = 0.6892 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 06:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.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 06:18:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:18:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:18:49: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:18:49: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:18:49: #1 total tags in treatment: 187130 INFO @ Sat, 11 Dec 2021 06:18:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:18:49: #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 06:18:49: #1 tags after filtering in treatment: 163883 INFO @ Sat, 11 Dec 2021 06:18:49: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:18:49: #1 finished! INFO @ Sat, 11 Dec 2021 06:18:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:18:49: #2 number of paired peaks: 2732 INFO @ Sat, 11 Dec 2021 06:18:49: start model_add_line... INFO @ Sat, 11 Dec 2021 06:18:49: start X-correlation... INFO @ Sat, 11 Dec 2021 06:18:49: end of X-cor INFO @ Sat, 11 Dec 2021 06:18:49: #2 finished! INFO @ Sat, 11 Dec 2021 06:18:49: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 06:18:49: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 06:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.05_model.r WARNING @ Sat, 11 Dec 2021 06:18:49: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:18:49: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 06:18:49: #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 06:18:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:18:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:18:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:18:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:18:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.05_summits.bed INFO @ Sat, 11 Dec 2021 06:18:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (609 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 06:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.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 06:19:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:19:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:19:18: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:19:18: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:19:18: #1 total tags in treatment: 187130 INFO @ Sat, 11 Dec 2021 06:19:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:19:18: #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 06:19:18: #1 tags after filtering in treatment: 163883 INFO @ Sat, 11 Dec 2021 06:19:18: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:19:18: #1 finished! INFO @ Sat, 11 Dec 2021 06:19:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:19:18: #2 number of paired peaks: 2732 INFO @ Sat, 11 Dec 2021 06:19:18: start model_add_line... INFO @ Sat, 11 Dec 2021 06:19:18: start X-correlation... INFO @ Sat, 11 Dec 2021 06:19:18: end of X-cor INFO @ Sat, 11 Dec 2021 06:19:18: #2 finished! INFO @ Sat, 11 Dec 2021 06:19:18: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 06:19:18: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 06:19:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.10_model.r WARNING @ Sat, 11 Dec 2021 06:19:18: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:19:18: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 06:19:18: #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 06:19:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:19:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.10_summits.bed INFO @ Sat, 11 Dec 2021 06:19:19: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 6 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 06:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.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 06:19:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:19:39: #1 read treatment tags... 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 06:19:48: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:19:48: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:19:48: #1 total tags in treatment: 187130 INFO @ Sat, 11 Dec 2021 06:19:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:19:48: #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 06:19:48: #1 tags after filtering in treatment: 163883 INFO @ Sat, 11 Dec 2021 06:19:48: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:19:48: #1 finished! INFO @ Sat, 11 Dec 2021 06:19:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:19:48: #2 number of paired peaks: 2732 INFO @ Sat, 11 Dec 2021 06:19:48: start model_add_line... INFO @ Sat, 11 Dec 2021 06:19:48: start X-correlation... INFO @ Sat, 11 Dec 2021 06:19:48: end of X-cor INFO @ Sat, 11 Dec 2021 06:19:48: #2 finished! INFO @ Sat, 11 Dec 2021 06:19:48: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 06:19:48: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 06:19:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.20_model.r WARNING @ Sat, 11 Dec 2021 06:19:48: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:19:48: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 06:19:48: #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 06:19:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:19:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:19:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556390/SRX8556390.20_summits.bed INFO @ Sat, 11 Dec 2021 06:19:49: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 1 millis CompletedMACS2peakCalling