Job ID = 12266682 SRX = SRX8622117 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 79943221 spots for SRR12096677/SRR12096677.sra Written 79943221 spots for SRR12096677/SRR12096677.sra fastq に変換しました。 bowtie でマッピング中... Your job 12269967 ("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: 02:02:16 79943221 reads; of these: 79943221 (100.00%) were paired; of these: 73135728 (91.48%) aligned concordantly 0 times 4746834 (5.94%) aligned concordantly exactly 1 time 2060659 (2.58%) aligned concordantly >1 times ---- 73135728 pairs aligned concordantly 0 times; of these: 2473397 (3.38%) aligned discordantly 1 time ---- 70662331 pairs aligned 0 times concordantly or discordantly; of these: 141324662 mates make up the pairs; of these: 138325192 (97.88%) aligned 0 times 857202 (0.61%) aligned exactly 1 time 2142268 (1.52%) aligned >1 times 13.49% overall alignment rate Time searching: 02:02:16 Overall time: 02:02:16 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 16 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] 1781328 / 9170594 = 0.1942 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 11:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.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, 03 Apr 2021 11:38:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 11:38:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 11:38:25: 1000000 INFO @ Sat, 03 Apr 2021 11:38:34: 2000000 INFO @ Sat, 03 Apr 2021 11:38:43: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 11:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.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, 03 Apr 2021 11:38:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 11:38:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 11:38:53: 4000000 INFO @ Sat, 03 Apr 2021 11:38:56: 1000000 INFO @ Sat, 03 Apr 2021 11:39:03: 5000000 INFO @ Sat, 03 Apr 2021 11:39:07: 2000000 BedGraph に変換中... INFO @ Sat, 03 Apr 2021 11:39:14: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 11:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.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, 03 Apr 2021 11:39:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 11:39:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 11:39:17: 3000000 INFO @ Sat, 03 Apr 2021 11:39:24: 7000000 INFO @ Sat, 03 Apr 2021 11:39:26: 1000000 INFO @ Sat, 03 Apr 2021 11:39:28: 4000000 INFO @ Sat, 03 Apr 2021 11:39:35: 8000000 INFO @ Sat, 03 Apr 2021 11:39:37: 2000000 INFO @ Sat, 03 Apr 2021 11:39:38: 5000000 INFO @ Sat, 03 Apr 2021 11:39:45: 9000000 INFO @ Sat, 03 Apr 2021 11:39:47: 3000000 INFO @ Sat, 03 Apr 2021 11:39:48: 6000000 INFO @ Sat, 03 Apr 2021 11:39:55: 10000000 INFO @ Sat, 03 Apr 2021 11:39:57: 4000000 INFO @ Sat, 03 Apr 2021 11:39:59: 7000000 INFO @ Sat, 03 Apr 2021 11:40:05: 11000000 INFO @ Sat, 03 Apr 2021 11:40:08: 5000000 INFO @ Sat, 03 Apr 2021 11:40:09: 8000000 INFO @ Sat, 03 Apr 2021 11:40:15: 12000000 INFO @ Sat, 03 Apr 2021 11:40:18: 6000000 INFO @ Sat, 03 Apr 2021 11:40:19: 9000000 INFO @ Sat, 03 Apr 2021 11:40:26: 13000000 INFO @ Sat, 03 Apr 2021 11:40:28: 7000000 INFO @ Sat, 03 Apr 2021 11:40:29: 10000000 INFO @ Sat, 03 Apr 2021 11:40:36: 14000000 INFO @ Sat, 03 Apr 2021 11:40:39: 8000000 INFO @ Sat, 03 Apr 2021 11:40:40: 11000000 INFO @ Sat, 03 Apr 2021 11:40:46: 15000000 INFO @ Sat, 03 Apr 2021 11:40:49: 9000000 INFO @ Sat, 03 Apr 2021 11:40:50: 12000000 INFO @ Sat, 03 Apr 2021 11:40:57: 16000000 INFO @ Sat, 03 Apr 2021 11:40:59: 10000000 INFO @ Sat, 03 Apr 2021 11:41:00: 13000000 INFO @ Sat, 03 Apr 2021 11:41:08: 17000000 INFO @ Sat, 03 Apr 2021 11:41:10: 11000000 INFO @ Sat, 03 Apr 2021 11:41:11: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 11:41:18: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 11:41:18: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 11:41:18: #1 total tags in treatment: 5507399 INFO @ Sat, 03 Apr 2021 11:41:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 11:41:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 11:41:18: #1 tags after filtering in treatment: 4828626 INFO @ Sat, 03 Apr 2021 11:41:18: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 11:41:18: #1 finished! INFO @ Sat, 03 Apr 2021 11:41:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 11:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 11:41:19: #2 number of paired peaks: 464 WARNING @ Sat, 03 Apr 2021 11:41:19: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sat, 03 Apr 2021 11:41:19: start model_add_line... INFO @ Sat, 03 Apr 2021 11:41:19: start X-correlation... INFO @ Sat, 03 Apr 2021 11:41:19: end of X-cor INFO @ Sat, 03 Apr 2021 11:41:19: #2 finished! INFO @ Sat, 03 Apr 2021 11:41:19: #2 predicted fragment length is 181 bps INFO @ Sat, 03 Apr 2021 11:41:19: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 03 Apr 2021 11:41:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.05_model.r WARNING @ Sat, 03 Apr 2021 11:41:19: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 11:41:19: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 03 Apr 2021 11:41:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 11:41:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 11:41:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 11:41:20: 12000000 INFO @ Sat, 03 Apr 2021 11:41:21: 15000000 INFO @ Sat, 03 Apr 2021 11:41:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 11:41:31: 13000000 INFO @ Sat, 03 Apr 2021 11:41:32: 16000000 INFO @ Sat, 03 Apr 2021 11:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.05_peaks.xls INFO @ Sat, 03 Apr 2021 11:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 11:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.05_summits.bed INFO @ Sat, 03 Apr 2021 11:41:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3445 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 11:41:42: 14000000 INFO @ Sat, 03 Apr 2021 11:41:43: 17000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 11:41:53: 15000000 INFO @ Sat, 03 Apr 2021 11:41:54: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 11:41:54: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 11:41:54: #1 total tags in treatment: 5507399 INFO @ Sat, 03 Apr 2021 11:41:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 11:41:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 11:41:54: #1 tags after filtering in treatment: 4828626 INFO @ Sat, 03 Apr 2021 11:41:54: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 11:41:54: #1 finished! INFO @ Sat, 03 Apr 2021 11:41:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 11:41:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 11:41:54: #2 number of paired peaks: 464 WARNING @ Sat, 03 Apr 2021 11:41:54: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sat, 03 Apr 2021 11:41:54: start model_add_line... INFO @ Sat, 03 Apr 2021 11:41:54: start X-correlation... INFO @ Sat, 03 Apr 2021 11:41:54: end of X-cor INFO @ Sat, 03 Apr 2021 11:41:54: #2 finished! INFO @ Sat, 03 Apr 2021 11:41:54: #2 predicted fragment length is 181 bps INFO @ Sat, 03 Apr 2021 11:41:54: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 03 Apr 2021 11:41:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.10_model.r WARNING @ Sat, 03 Apr 2021 11:41:54: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 11:41:54: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 03 Apr 2021 11:41:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 11:41:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 11:41:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 11:42:03: 16000000 INFO @ Sat, 03 Apr 2021 11:42:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 11:42:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.10_peaks.xls INFO @ Sat, 03 Apr 2021 11:42:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 11:42:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.10_summits.bed INFO @ Sat, 03 Apr 2021 11:42:12: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1373 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 11:42:13: 17000000 INFO @ Sat, 03 Apr 2021 11:42:22: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 11:42:22: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 11:42:22: #1 total tags in treatment: 5507399 INFO @ Sat, 03 Apr 2021 11:42:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 11:42:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 11:42:22: #1 tags after filtering in treatment: 4828626 INFO @ Sat, 03 Apr 2021 11:42:22: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 11:42:22: #1 finished! INFO @ Sat, 03 Apr 2021 11:42:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 11:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 11:42:23: #2 number of paired peaks: 464 WARNING @ Sat, 03 Apr 2021 11:42:23: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sat, 03 Apr 2021 11:42:23: start model_add_line... INFO @ Sat, 03 Apr 2021 11:42:23: start X-correlation... INFO @ Sat, 03 Apr 2021 11:42:23: end of X-cor INFO @ Sat, 03 Apr 2021 11:42:23: #2 finished! INFO @ Sat, 03 Apr 2021 11:42:23: #2 predicted fragment length is 181 bps INFO @ Sat, 03 Apr 2021 11:42:23: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 03 Apr 2021 11:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.20_model.r WARNING @ Sat, 03 Apr 2021 11:42:23: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 11:42:23: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 03 Apr 2021 11:42:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 11:42:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 11:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 11:42:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 11:42:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.20_peaks.xls INFO @ Sat, 03 Apr 2021 11:42:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 11:42:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622117/SRX8622117.20_summits.bed INFO @ Sat, 03 Apr 2021 11:42:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 2 millis CompletedMACS2peakCalling