Job ID = 14170589 SRX = SRX8497047 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12866479 spots for SRR11952646/SRR11952646.sra Written 12866479 spots for SRR11952646/SRR11952646.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171056 ("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: 00:21:15 12866479 reads; of these: 12866479 (100.00%) were paired; of these: 7928411 (61.62%) aligned concordantly 0 times 3041997 (23.64%) aligned concordantly exactly 1 time 1896071 (14.74%) aligned concordantly >1 times ---- 7928411 pairs aligned concordantly 0 times; of these: 135814 (1.71%) aligned discordantly 1 time ---- 7792597 pairs aligned 0 times concordantly or discordantly; of these: 15585194 mates make up the pairs; of these: 15242791 (97.80%) aligned 0 times 141862 (0.91%) aligned exactly 1 time 200541 (1.29%) aligned >1 times 40.77% overall alignment rate Time searching: 00:21:15 Overall time: 00:21:15 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] 1549356 / 5063687 = 0.3060 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 07:49:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.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 07:49:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:49:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:49:41: 1000000 INFO @ Sat, 11 Dec 2021 07:49:47: 2000000 INFO @ Sat, 11 Dec 2021 07:49:53: 3000000 INFO @ Sat, 11 Dec 2021 07:49:59: 4000000 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 07:50:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.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 07:50:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:50:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:50:05: 5000000 INFO @ Sat, 11 Dec 2021 07:50:11: 6000000 INFO @ Sat, 11 Dec 2021 07:50:12: 1000000 INFO @ Sat, 11 Dec 2021 07:50:18: 7000000 INFO @ Sat, 11 Dec 2021 07:50:20: 2000000 INFO @ Sat, 11 Dec 2021 07:50:20: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:50:20: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:50:20: #1 total tags in treatment: 3417176 INFO @ Sat, 11 Dec 2021 07:50:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:50:20: #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 07:50:20: #1 tags after filtering in treatment: 2983363 INFO @ Sat, 11 Dec 2021 07:50:20: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 07:50:20: #1 finished! INFO @ Sat, 11 Dec 2021 07:50:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:50:21: #2 number of paired peaks: 503 WARNING @ Sat, 11 Dec 2021 07:50:21: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Sat, 11 Dec 2021 07:50:21: start model_add_line... INFO @ Sat, 11 Dec 2021 07:50:21: start X-correlation... INFO @ Sat, 11 Dec 2021 07:50:21: end of X-cor INFO @ Sat, 11 Dec 2021 07:50:21: #2 finished! INFO @ Sat, 11 Dec 2021 07:50:21: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 07:50:21: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 07:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.05_model.r WARNING @ Sat, 11 Dec 2021 07:50:21: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:50:21: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 07:50:21: #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 07:50:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:50:27: 3000000 INFO @ Sat, 11 Dec 2021 07:50:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.05_summits.bed INFO @ Sat, 11 Dec 2021 07:50:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1228 records, 4 fields): 5 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 07:50:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.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 07:50:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:50:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:50:34: 4000000 INFO @ Sat, 11 Dec 2021 07:50:42: 5000000 INFO @ Sat, 11 Dec 2021 07:50:42: 1000000 INFO @ Sat, 11 Dec 2021 07:50:50: 6000000 INFO @ Sat, 11 Dec 2021 07:50:51: 2000000 INFO @ Sat, 11 Dec 2021 07:50:58: 7000000 INFO @ Sat, 11 Dec 2021 07:51:00: 3000000 INFO @ Sat, 11 Dec 2021 07:51:02: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:51:02: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:51:02: #1 total tags in treatment: 3417176 INFO @ Sat, 11 Dec 2021 07:51:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:51:02: #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 07:51:02: #1 tags after filtering in treatment: 2983363 INFO @ Sat, 11 Dec 2021 07:51:02: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 07:51:02: #1 finished! INFO @ Sat, 11 Dec 2021 07:51:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:51:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:51:02: #2 number of paired peaks: 503 WARNING @ Sat, 11 Dec 2021 07:51:02: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Sat, 11 Dec 2021 07:51:02: start model_add_line... INFO @ Sat, 11 Dec 2021 07:51:02: start X-correlation... INFO @ Sat, 11 Dec 2021 07:51:02: end of X-cor INFO @ Sat, 11 Dec 2021 07:51:02: #2 finished! INFO @ Sat, 11 Dec 2021 07:51:02: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 07:51:02: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 07:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.10_model.r WARNING @ Sat, 11 Dec 2021 07:51:02: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:51:02: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 07:51:02: #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 07:51:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:51:07: 4000000 INFO @ Sat, 11 Dec 2021 07:51:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:51:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.10_summits.bed INFO @ Sat, 11 Dec 2021 07:51:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:51:14: 5000000 INFO @ Sat, 11 Dec 2021 07:51:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:51:28: 7000000 INFO @ Sat, 11 Dec 2021 07:51:31: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:51:31: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:51:31: #1 total tags in treatment: 3417176 INFO @ Sat, 11 Dec 2021 07:51:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:51:31: #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 07:51:31: #1 tags after filtering in treatment: 2983363 INFO @ Sat, 11 Dec 2021 07:51:31: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 07:51:31: #1 finished! INFO @ Sat, 11 Dec 2021 07:51:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:51:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:51:31: #2 number of paired peaks: 503 WARNING @ Sat, 11 Dec 2021 07:51:31: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Sat, 11 Dec 2021 07:51:31: start model_add_line... INFO @ Sat, 11 Dec 2021 07:51:32: start X-correlation... INFO @ Sat, 11 Dec 2021 07:51:32: end of X-cor INFO @ Sat, 11 Dec 2021 07:51:32: #2 finished! INFO @ Sat, 11 Dec 2021 07:51:32: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 07:51:32: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 07:51:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.20_model.r WARNING @ Sat, 11 Dec 2021 07:51:32: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:51:32: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 07:51:32: #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 07:51:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:51:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:51:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497047/SRX8497047.20_summits.bed INFO @ Sat, 11 Dec 2021 07:51:42: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。