Job ID = 14170020 SRX = SRX8556350 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10592452 spots for SRR12024960/SRR12024960.sra Written 10592452 spots for SRR12024960/SRR12024960.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170652 ("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: 00:21:19 10592452 reads; of these: 10592452 (100.00%) were paired; of these: 8246624 (77.85%) aligned concordantly 0 times 943346 (8.91%) aligned concordantly exactly 1 time 1402482 (13.24%) aligned concordantly >1 times ---- 8246624 pairs aligned concordantly 0 times; of these: 256312 (3.11%) aligned discordantly 1 time ---- 7990312 pairs aligned 0 times concordantly or discordantly; of these: 15980624 mates make up the pairs; of these: 14089804 (88.17%) aligned 0 times 562454 (3.52%) aligned exactly 1 time 1328366 (8.31%) aligned >1 times 33.49% overall alignment rate Time searching: 00:21:21 Overall time: 00:21:21 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] 894155 / 2535088 = 0.3527 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 05:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.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 05:05:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:05:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:05:10: 1000000 INFO @ Sat, 11 Dec 2021 05:05:18: 2000000 INFO @ Sat, 11 Dec 2021 05:05:26: 3000000 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 05:05:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.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 05:05:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:05:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:05:35: 4000000 INFO @ Sat, 11 Dec 2021 05:05:42: 1000000 INFO @ Sat, 11 Dec 2021 05:05:45: 5000000 INFO @ Sat, 11 Dec 2021 05:05:48: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:05:48: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:05:48: #1 total tags in treatment: 1503498 INFO @ Sat, 11 Dec 2021 05:05:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:05:48: #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 05:05:48: #1 tags after filtering in treatment: 1008950 INFO @ Sat, 11 Dec 2021 05:05:48: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 05:05:48: #1 finished! INFO @ Sat, 11 Dec 2021 05:05:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:05:48: #2 number of paired peaks: 874 WARNING @ Sat, 11 Dec 2021 05:05:48: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 11 Dec 2021 05:05:48: start model_add_line... INFO @ Sat, 11 Dec 2021 05:05:48: start X-correlation... INFO @ Sat, 11 Dec 2021 05:05:48: end of X-cor INFO @ Sat, 11 Dec 2021 05:05:48: #2 finished! INFO @ Sat, 11 Dec 2021 05:05:48: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 05:05:48: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 05:05:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.05_model.r WARNING @ Sat, 11 Dec 2021 05:05:48: #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 05:05:48: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 05:05:48: #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 05:05:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:05:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:05:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:05:51: 2000000 INFO @ Sat, 11 Dec 2021 05:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.05_peaks.xls INFO @ Sat, 11 Dec 2021 05:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.05_summits.bed INFO @ Sat, 11 Dec 2021 05:05:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (870 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 05:06:00: 3000000 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 05:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.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 05:06:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:06:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:06:10: 4000000 INFO @ Sat, 11 Dec 2021 05:06:14: 1000000 INFO @ Sat, 11 Dec 2021 05:06:21: 5000000 INFO @ Sat, 11 Dec 2021 05:06:24: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:06:24: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:06:24: #1 total tags in treatment: 1503498 INFO @ Sat, 11 Dec 2021 05:06:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:06:24: #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 05:06:24: #1 tags after filtering in treatment: 1008950 INFO @ Sat, 11 Dec 2021 05:06:24: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 05:06:24: #1 finished! INFO @ Sat, 11 Dec 2021 05:06:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:06:24: #2 number of paired peaks: 874 WARNING @ Sat, 11 Dec 2021 05:06:24: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 11 Dec 2021 05:06:24: start model_add_line... INFO @ Sat, 11 Dec 2021 05:06:24: start X-correlation... INFO @ Sat, 11 Dec 2021 05:06:24: end of X-cor INFO @ Sat, 11 Dec 2021 05:06:24: #2 finished! INFO @ Sat, 11 Dec 2021 05:06:24: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 05:06:24: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 05:06:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.10_model.r WARNING @ Sat, 11 Dec 2021 05:06:24: #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 05:06:24: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 05:06:24: #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 05:06:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:06:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:06:25: 2000000 INFO @ Sat, 11 Dec 2021 05:06:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.10_peaks.xls INFO @ Sat, 11 Dec 2021 05:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:06:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.10_summits.bed INFO @ Sat, 11 Dec 2021 05:06:28: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 05:06:35: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 05:06:45: 4000000 INFO @ Sat, 11 Dec 2021 05:06:56: 5000000 INFO @ Sat, 11 Dec 2021 05:06:59: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:06:59: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:06:59: #1 total tags in treatment: 1503498 INFO @ Sat, 11 Dec 2021 05:06:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:06:59: #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 05:06:59: #1 tags after filtering in treatment: 1008950 INFO @ Sat, 11 Dec 2021 05:06:59: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 05:06:59: #1 finished! INFO @ Sat, 11 Dec 2021 05:06:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:06:59: #2 number of paired peaks: 874 WARNING @ Sat, 11 Dec 2021 05:06:59: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 11 Dec 2021 05:06:59: start model_add_line... INFO @ Sat, 11 Dec 2021 05:06:59: start X-correlation... INFO @ Sat, 11 Dec 2021 05:06:59: end of X-cor INFO @ Sat, 11 Dec 2021 05:06:59: #2 finished! INFO @ Sat, 11 Dec 2021 05:06:59: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 05:06:59: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 05:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.20_model.r WARNING @ Sat, 11 Dec 2021 05:06:59: #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 05:06:59: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 05:06:59: #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 05:06:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:07:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.20_peaks.xls INFO @ Sat, 11 Dec 2021 05:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556350/SRX8556350.20_summits.bed INFO @ Sat, 11 Dec 2021 05:07:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (480 records, 4 fields): 2 millis CompletedMACS2peakCalling