Job ID = 12265184 SRX = SRX3282117 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 42215974 spots for SRR6171268/SRR6171268.sra Written 42215974 spots for SRR6171268/SRR6171268.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265762 ("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: 01:09:04 42215974 reads; of these: 42215974 (100.00%) were paired; of these: 28213455 (66.83%) aligned concordantly 0 times 7036773 (16.67%) aligned concordantly exactly 1 time 6965746 (16.50%) aligned concordantly >1 times ---- 28213455 pairs aligned concordantly 0 times; of these: 1319260 (4.68%) aligned discordantly 1 time ---- 26894195 pairs aligned 0 times concordantly or discordantly; of these: 53788390 mates make up the pairs; of these: 51297710 (95.37%) aligned 0 times 439028 (0.82%) aligned exactly 1 time 2051652 (3.81%) aligned >1 times 39.24% overall alignment rate Time searching: 01:09:04 Overall time: 01:09:04 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] 5038846 / 15207397 = 0.3313 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 08:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.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 08:10:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:10:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:10:19: 1000000 INFO @ Sat, 03 Apr 2021 08:10:28: 2000000 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 08:10:38: 3000000 INFO @ Sat, 03 Apr 2021 08:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.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 08:10:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:10:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:10:48: 4000000 INFO @ Sat, 03 Apr 2021 08:10:50: 1000000 INFO @ Sat, 03 Apr 2021 08:10:59: 5000000 INFO @ Sat, 03 Apr 2021 08:11:01: 2000000 BedGraph に変換中... 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 08:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.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 08:11:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:11:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:11:10: 6000000 INFO @ Sat, 03 Apr 2021 08:11:12: 3000000 INFO @ Sat, 03 Apr 2021 08:11:21: 1000000 INFO @ Sat, 03 Apr 2021 08:11:22: 7000000 INFO @ Sat, 03 Apr 2021 08:11:24: 4000000 INFO @ Sat, 03 Apr 2021 08:11:34: 2000000 INFO @ Sat, 03 Apr 2021 08:11:34: 8000000 INFO @ Sat, 03 Apr 2021 08:11:36: 5000000 INFO @ Sat, 03 Apr 2021 08:11:46: 9000000 INFO @ Sat, 03 Apr 2021 08:11:46: 3000000 INFO @ Sat, 03 Apr 2021 08:11:48: 6000000 INFO @ Sat, 03 Apr 2021 08:11:57: 10000000 INFO @ Sat, 03 Apr 2021 08:11:58: 4000000 INFO @ Sat, 03 Apr 2021 08:12:00: 7000000 INFO @ Sat, 03 Apr 2021 08:12:09: 11000000 INFO @ Sat, 03 Apr 2021 08:12:11: 5000000 INFO @ Sat, 03 Apr 2021 08:12:11: 8000000 INFO @ Sat, 03 Apr 2021 08:12:20: 12000000 INFO @ Sat, 03 Apr 2021 08:12:23: 6000000 INFO @ Sat, 03 Apr 2021 08:12:23: 9000000 INFO @ Sat, 03 Apr 2021 08:12:32: 13000000 INFO @ Sat, 03 Apr 2021 08:12:35: 10000000 INFO @ Sat, 03 Apr 2021 08:12:35: 7000000 INFO @ Sat, 03 Apr 2021 08:12:44: 14000000 INFO @ Sat, 03 Apr 2021 08:12:46: 11000000 INFO @ Sat, 03 Apr 2021 08:12:47: 8000000 INFO @ Sat, 03 Apr 2021 08:12:54: 15000000 INFO @ Sat, 03 Apr 2021 08:12:57: 12000000 INFO @ Sat, 03 Apr 2021 08:13:00: 9000000 INFO @ Sat, 03 Apr 2021 08:13:04: 16000000 INFO @ Sat, 03 Apr 2021 08:13:08: 13000000 INFO @ Sat, 03 Apr 2021 08:13:12: 10000000 INFO @ Sat, 03 Apr 2021 08:13:15: 17000000 INFO @ Sat, 03 Apr 2021 08:13:19: 14000000 INFO @ Sat, 03 Apr 2021 08:13:24: 11000000 INFO @ Sat, 03 Apr 2021 08:13:25: 18000000 INFO @ Sat, 03 Apr 2021 08:13:30: 15000000 INFO @ Sat, 03 Apr 2021 08:13:36: 19000000 INFO @ Sat, 03 Apr 2021 08:13:36: 12000000 INFO @ Sat, 03 Apr 2021 08:13:39: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:13:45: 20000000 INFO @ Sat, 03 Apr 2021 08:13:48: 13000000 INFO @ Sat, 03 Apr 2021 08:13:49: 17000000 INFO @ Sat, 03 Apr 2021 08:13:55: 21000000 INFO @ Sat, 03 Apr 2021 08:13:58: 18000000 INFO @ Sat, 03 Apr 2021 08:13:59: 14000000 INFO @ Sat, 03 Apr 2021 08:14:04: 22000000 INFO @ Sat, 03 Apr 2021 08:14:08: 19000000 INFO @ Sat, 03 Apr 2021 08:14:10: 15000000 INFO @ Sat, 03 Apr 2021 08:14:14: 23000000 INFO @ Sat, 03 Apr 2021 08:14:14: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 08:14:14: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 08:14:14: #1 total tags in treatment: 9094168 INFO @ Sat, 03 Apr 2021 08:14:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:14:14: #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 08:14:14: #1 tags after filtering in treatment: 7041398 INFO @ Sat, 03 Apr 2021 08:14:14: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 08:14:14: #1 finished! INFO @ Sat, 03 Apr 2021 08:14:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:14:15: #2 number of paired peaks: 1083 INFO @ Sat, 03 Apr 2021 08:14:15: start model_add_line... INFO @ Sat, 03 Apr 2021 08:14:15: start X-correlation... INFO @ Sat, 03 Apr 2021 08:14:15: end of X-cor INFO @ Sat, 03 Apr 2021 08:14:15: #2 finished! INFO @ Sat, 03 Apr 2021 08:14:15: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Apr 2021 08:14:15: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 03 Apr 2021 08:14:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.05_model.r WARNING @ Sat, 03 Apr 2021 08:14:15: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:14:15: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sat, 03 Apr 2021 08:14:15: #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 08:14:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:14:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:14:17: 20000000 INFO @ Sat, 03 Apr 2021 08:14:21: 16000000 INFO @ Sat, 03 Apr 2021 08:14:27: 21000000 INFO @ Sat, 03 Apr 2021 08:14:32: 17000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:14:36: 22000000 INFO @ Sat, 03 Apr 2021 08:14:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:14:43: 18000000 INFO @ Sat, 03 Apr 2021 08:14:45: 23000000 INFO @ Sat, 03 Apr 2021 08:14:45: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 08:14:45: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 08:14:45: #1 total tags in treatment: 9094168 INFO @ Sat, 03 Apr 2021 08:14:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:14:45: #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 08:14:45: #1 tags after filtering in treatment: 7041398 INFO @ Sat, 03 Apr 2021 08:14:45: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 08:14:45: #1 finished! INFO @ Sat, 03 Apr 2021 08:14:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:14:46: #2 number of paired peaks: 1083 INFO @ Sat, 03 Apr 2021 08:14:46: start model_add_line... INFO @ Sat, 03 Apr 2021 08:14:46: start X-correlation... INFO @ Sat, 03 Apr 2021 08:14:46: end of X-cor INFO @ Sat, 03 Apr 2021 08:14:46: #2 finished! INFO @ Sat, 03 Apr 2021 08:14:46: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Apr 2021 08:14:46: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 03 Apr 2021 08:14:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.10_model.r WARNING @ Sat, 03 Apr 2021 08:14:46: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:14:46: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sat, 03 Apr 2021 08:14:46: #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 08:14:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:14:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:14:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:14:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:14:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.05_summits.bed INFO @ Sat, 03 Apr 2021 08:14:48: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6829 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:14:54: 19000000 INFO @ Sat, 03 Apr 2021 08:15:05: 20000000 INFO @ Sat, 03 Apr 2021 08:15:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:15:16: 21000000 INFO @ Sat, 03 Apr 2021 08:15:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:15:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:15:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.10_summits.bed INFO @ Sat, 03 Apr 2021 08:15:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3487 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:15:26: 22000000 INFO @ Sat, 03 Apr 2021 08:15:36: 23000000 INFO @ Sat, 03 Apr 2021 08:15:37: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 08:15:37: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 08:15:37: #1 total tags in treatment: 9094168 INFO @ Sat, 03 Apr 2021 08:15:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:15:37: #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 08:15:37: #1 tags after filtering in treatment: 7041398 INFO @ Sat, 03 Apr 2021 08:15:37: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 08:15:37: #1 finished! INFO @ Sat, 03 Apr 2021 08:15:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:15:38: #2 number of paired peaks: 1083 INFO @ Sat, 03 Apr 2021 08:15:38: start model_add_line... INFO @ Sat, 03 Apr 2021 08:15:38: start X-correlation... INFO @ Sat, 03 Apr 2021 08:15:38: end of X-cor INFO @ Sat, 03 Apr 2021 08:15:38: #2 finished! INFO @ Sat, 03 Apr 2021 08:15:38: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Apr 2021 08:15:38: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 03 Apr 2021 08:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.20_model.r WARNING @ Sat, 03 Apr 2021 08:15:38: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:15:38: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sat, 03 Apr 2021 08:15:38: #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 08:15:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:15:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282117/SRX3282117.20_summits.bed INFO @ Sat, 03 Apr 2021 08:16:10: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1255 records, 4 fields): 6 millis CompletedMACS2peakCalling