Job ID = 14170112 SRX = SRX8556370 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25670614 spots for SRR12024926/SRR12024926.sra Written 25670614 spots for SRR12024926/SRR12024926.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170702 ("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: 00:24:17 25670614 reads; of these: 25670614 (100.00%) were paired; of these: 22812355 (88.87%) aligned concordantly 0 times 1869771 (7.28%) aligned concordantly exactly 1 time 988488 (3.85%) aligned concordantly >1 times ---- 22812355 pairs aligned concordantly 0 times; of these: 352279 (1.54%) aligned discordantly 1 time ---- 22460076 pairs aligned 0 times concordantly or discordantly; of these: 44920152 mates make up the pairs; of these: 44414838 (98.88%) aligned 0 times 120719 (0.27%) aligned exactly 1 time 384595 (0.86%) aligned >1 times 13.49% overall alignment rate Time searching: 00:24:17 Overall time: 00:24:17 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] 2141173 / 3181753 = 0.6730 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 05:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.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 05:58:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:58:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:58:19: 1000000 INFO @ Sat, 11 Dec 2021 05:58:29: 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 @ Sat, 11 Dec 2021 05:58:36: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:58:36: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:58:36: #1 total tags in treatment: 893690 INFO @ Sat, 11 Dec 2021 05:58:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:58:36: #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 05:58:36: #1 tags after filtering in treatment: 820247 INFO @ Sat, 11 Dec 2021 05:58:36: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 05:58:36: #1 finished! INFO @ Sat, 11 Dec 2021 05:58:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:58:37: #2 number of paired peaks: 2389 INFO @ Sat, 11 Dec 2021 05:58:37: start model_add_line... INFO @ Sat, 11 Dec 2021 05:58:37: start X-correlation... INFO @ Sat, 11 Dec 2021 05:58:37: end of X-cor INFO @ Sat, 11 Dec 2021 05:58:37: #2 finished! INFO @ Sat, 11 Dec 2021 05:58:37: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 05:58:37: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 11 Dec 2021 05:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.05_model.r WARNING @ Sat, 11 Dec 2021 05:58:37: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:58:37: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 11 Dec 2021 05:58:37: #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 05:58:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.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 05:58:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:58:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:58:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.05_peaks.xls INFO @ Sat, 11 Dec 2021 05:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.05_summits.bed INFO @ Sat, 11 Dec 2021 05:58:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1355 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 05:58:47: 1000000 INFO @ Sat, 11 Dec 2021 05:58:57: 2000000 INFO @ Sat, 11 Dec 2021 05:59:05: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:59:05: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:59:05: #1 total tags in treatment: 893690 INFO @ Sat, 11 Dec 2021 05:59:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:59:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Sat, 11 Dec 2021 05:59:05: #1 tags after filtering in treatment: 820247 INFO @ Sat, 11 Dec 2021 05:59:05: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 05:59:05: #1 finished! INFO @ Sat, 11 Dec 2021 05:59:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:59:05: #2 looking for paired plus/minus strand peaks... 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 05:59:05: #2 number of paired peaks: 2389 INFO @ Sat, 11 Dec 2021 05:59:05: start model_add_line... INFO @ Sat, 11 Dec 2021 05:59:05: start X-correlation... INFO @ Sat, 11 Dec 2021 05:59:05: end of X-cor INFO @ Sat, 11 Dec 2021 05:59:05: #2 finished! INFO @ Sat, 11 Dec 2021 05:59:05: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 05:59:05: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 11 Dec 2021 05:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.10_model.r WARNING @ Sat, 11 Dec 2021 05:59:05: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:59:05: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 11 Dec 2021 05:59:05: #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 05:59:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:59:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.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 05:59:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:59:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.10_peaks.xls INFO @ Sat, 11 Dec 2021 05:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.10_summits.bed INFO @ Sat, 11 Dec 2021 05:59:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (500 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 05:59:18: 1000000 INFO @ Sat, 11 Dec 2021 05:59:28: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 05:59:35: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:59:35: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:59:35: #1 total tags in treatment: 893690 INFO @ Sat, 11 Dec 2021 05:59:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:59:35: #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 05:59:35: #1 tags after filtering in treatment: 820247 INFO @ Sat, 11 Dec 2021 05:59:35: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 05:59:35: #1 finished! INFO @ Sat, 11 Dec 2021 05:59:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:59:35: #2 number of paired peaks: 2389 INFO @ Sat, 11 Dec 2021 05:59:35: start model_add_line... INFO @ Sat, 11 Dec 2021 05:59:35: start X-correlation... INFO @ Sat, 11 Dec 2021 05:59:35: end of X-cor INFO @ Sat, 11 Dec 2021 05:59:35: #2 finished! INFO @ Sat, 11 Dec 2021 05:59:35: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 05:59:35: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 11 Dec 2021 05:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.20_model.r WARNING @ Sat, 11 Dec 2021 05:59:35: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:59:35: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 11 Dec 2021 05:59:35: #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 05:59:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:59:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 05:59:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.20_peaks.xls INFO @ Sat, 11 Dec 2021 05:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556370/SRX8556370.20_summits.bed INFO @ Sat, 11 Dec 2021 05:59:38: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 2 millis CompletedMACS2peakCalling