Job ID = 14171632 SRX = SRX9352514 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28992234 spots for SRR12887233/SRR12887233.sra Written 28992234 spots for SRR12887233/SRR12887233.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172523 ("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: 01:47:33 28992234 reads; of these: 28992234 (100.00%) were paired; of these: 3896668 (13.44%) aligned concordantly 0 times 18735269 (64.62%) aligned concordantly exactly 1 time 6360297 (21.94%) aligned concordantly >1 times ---- 3896668 pairs aligned concordantly 0 times; of these: 141627 (3.63%) aligned discordantly 1 time ---- 3755041 pairs aligned 0 times concordantly or discordantly; of these: 7510082 mates make up the pairs; of these: 5099840 (67.91%) aligned 0 times 843325 (11.23%) aligned exactly 1 time 1566917 (20.86%) aligned >1 times 91.20% overall alignment rate Time searching: 01:47:33 Overall time: 01:47:33 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 24 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] 16573156 / 24979123 = 0.6635 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 14:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.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 14:14:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:14:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:14:39: 1000000 INFO @ Sat, 11 Dec 2021 14:14:44: 2000000 INFO @ Sat, 11 Dec 2021 14:14:49: 3000000 INFO @ Sat, 11 Dec 2021 14:14:54: 4000000 INFO @ Sat, 11 Dec 2021 14:14:59: 5000000 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 14:15:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.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 14:15:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:15:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:15:04: 6000000 INFO @ Sat, 11 Dec 2021 14:15:09: 1000000 INFO @ Sat, 11 Dec 2021 14:15:09: 7000000 INFO @ Sat, 11 Dec 2021 14:15:14: 2000000 INFO @ Sat, 11 Dec 2021 14:15:15: 8000000 INFO @ Sat, 11 Dec 2021 14:15:20: 3000000 INFO @ Sat, 11 Dec 2021 14:15:20: 9000000 INFO @ Sat, 11 Dec 2021 14:15:25: 4000000 INFO @ Sat, 11 Dec 2021 14:15:25: 10000000 INFO @ Sat, 11 Dec 2021 14:15:30: 5000000 INFO @ Sat, 11 Dec 2021 14:15:31: 11000000 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 14:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.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 14:15:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:15:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:15:36: 6000000 INFO @ Sat, 11 Dec 2021 14:15:36: 12000000 INFO @ Sat, 11 Dec 2021 14:15:39: 1000000 INFO @ Sat, 11 Dec 2021 14:15:41: 7000000 INFO @ Sat, 11 Dec 2021 14:15:42: 13000000 INFO @ Sat, 11 Dec 2021 14:15:45: 2000000 INFO @ Sat, 11 Dec 2021 14:15:47: 8000000 INFO @ Sat, 11 Dec 2021 14:15:47: 14000000 INFO @ Sat, 11 Dec 2021 14:15:50: 3000000 INFO @ Sat, 11 Dec 2021 14:15:52: 9000000 INFO @ Sat, 11 Dec 2021 14:15:52: 15000000 INFO @ Sat, 11 Dec 2021 14:15:56: 4000000 INFO @ Sat, 11 Dec 2021 14:15:58: 10000000 INFO @ Sat, 11 Dec 2021 14:15:58: 16000000 INFO @ Sat, 11 Dec 2021 14:16:01: 5000000 INFO @ Sat, 11 Dec 2021 14:16:03: 11000000 INFO @ Sat, 11 Dec 2021 14:16:03: 17000000 INFO @ Sat, 11 Dec 2021 14:16:07: 6000000 INFO @ Sat, 11 Dec 2021 14:16:09: 12000000 INFO @ Sat, 11 Dec 2021 14:16:09: 18000000 INFO @ Sat, 11 Dec 2021 14:16:12: 7000000 INFO @ Sat, 11 Dec 2021 14:16:14: 19000000 INFO @ Sat, 11 Dec 2021 14:16:14: 13000000 INFO @ Sat, 11 Dec 2021 14:16:18: 8000000 INFO @ Sat, 11 Dec 2021 14:16:18: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 14:16:18: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 14:16:18: #1 total tags in treatment: 8565121 INFO @ Sat, 11 Dec 2021 14:16:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:16:18: #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 14:16:18: #1 tags after filtering in treatment: 7489938 INFO @ Sat, 11 Dec 2021 14:16:18: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 14:16:18: #1 finished! INFO @ Sat, 11 Dec 2021 14:16:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:16:19: #2 number of paired peaks: 734 WARNING @ Sat, 11 Dec 2021 14:16:19: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Sat, 11 Dec 2021 14:16:19: start model_add_line... INFO @ Sat, 11 Dec 2021 14:16:19: start X-correlation... INFO @ Sat, 11 Dec 2021 14:16:19: end of X-cor INFO @ Sat, 11 Dec 2021 14:16:19: #2 finished! INFO @ Sat, 11 Dec 2021 14:16:19: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 14:16:19: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 11 Dec 2021 14:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.05_model.r WARNING @ Sat, 11 Dec 2021 14:16:19: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:16:19: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 11 Dec 2021 14:16:19: #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 14:16:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:16:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:16:20: 14000000 INFO @ Sat, 11 Dec 2021 14:16:23: 9000000 INFO @ Sat, 11 Dec 2021 14:16:25: 15000000 INFO @ Sat, 11 Dec 2021 14:16:28: 10000000 INFO @ Sat, 11 Dec 2021 14:16:31: 16000000 INFO @ Sat, 11 Dec 2021 14:16:34: 11000000 INFO @ Sat, 11 Dec 2021 14:16:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:16:37: 17000000 INFO @ Sat, 11 Dec 2021 14:16:39: 12000000 INFO @ Sat, 11 Dec 2021 14:16:42: 18000000 INFO @ Sat, 11 Dec 2021 14:16:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:16:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:16:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.05_summits.bed INFO @ Sat, 11 Dec 2021 14:16:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5606 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:16:45: 13000000 INFO @ Sat, 11 Dec 2021 14:16:48: 19000000 INFO @ Sat, 11 Dec 2021 14:16:50: 14000000 INFO @ Sat, 11 Dec 2021 14:16:52: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 14:16:52: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 14:16:52: #1 total tags in treatment: 8565121 INFO @ Sat, 11 Dec 2021 14:16:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:16:52: #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 14:16:52: #1 tags after filtering in treatment: 7489938 INFO @ Sat, 11 Dec 2021 14:16:52: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 14:16:52: #1 finished! INFO @ Sat, 11 Dec 2021 14:16:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:16:52: #2 number of paired peaks: 734 WARNING @ Sat, 11 Dec 2021 14:16:52: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Sat, 11 Dec 2021 14:16:52: start model_add_line... INFO @ Sat, 11 Dec 2021 14:16:52: start X-correlation... INFO @ Sat, 11 Dec 2021 14:16:52: end of X-cor INFO @ Sat, 11 Dec 2021 14:16:52: #2 finished! INFO @ Sat, 11 Dec 2021 14:16:52: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 14:16:52: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 11 Dec 2021 14:16:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.10_model.r WARNING @ Sat, 11 Dec 2021 14:16:52: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:16:52: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 11 Dec 2021 14:16:52: #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 14:16:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:16:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:16:56: 15000000 INFO @ Sat, 11 Dec 2021 14:17:01: 16000000 INFO @ Sat, 11 Dec 2021 14:17:06: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:17:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:17:12: 18000000 INFO @ Sat, 11 Dec 2021 14:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.10_summits.bed INFO @ Sat, 11 Dec 2021 14:17:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2906 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:17:17: 19000000 INFO @ Sat, 11 Dec 2021 14:17:21: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 14:17:21: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 14:17:21: #1 total tags in treatment: 8565121 INFO @ Sat, 11 Dec 2021 14:17:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:17:21: #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 14:17:21: #1 tags after filtering in treatment: 7489938 INFO @ Sat, 11 Dec 2021 14:17:21: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 14:17:21: #1 finished! INFO @ Sat, 11 Dec 2021 14:17:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:17:21: #2 number of paired peaks: 734 WARNING @ Sat, 11 Dec 2021 14:17:21: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Sat, 11 Dec 2021 14:17:21: start model_add_line... INFO @ Sat, 11 Dec 2021 14:17:21: start X-correlation... INFO @ Sat, 11 Dec 2021 14:17:21: end of X-cor INFO @ Sat, 11 Dec 2021 14:17:21: #2 finished! INFO @ Sat, 11 Dec 2021 14:17:21: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 14:17:21: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 11 Dec 2021 14:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.20_model.r WARNING @ Sat, 11 Dec 2021 14:17:21: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:17:21: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 11 Dec 2021 14:17:21: #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 14:17:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:17:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9352514/SRX9352514.20_summits.bed INFO @ Sat, 11 Dec 2021 14:17:45: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1221 records, 4 fields): 4 millis CompletedMACS2peakCalling