Job ID = 12264847 SRX = SRX2789125 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 159975989 spots for SRR5515768/SRR5515768.sra Written 159975989 spots for SRR5515768/SRR5515768.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265670 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:57:40 159975989 reads; of these: 159975989 (100.00%) were paired; of these: 152434354 (95.29%) aligned concordantly 0 times 3580681 (2.24%) aligned concordantly exactly 1 time 3960954 (2.48%) aligned concordantly >1 times ---- 152434354 pairs aligned concordantly 0 times; of these: 1078641 (0.71%) aligned discordantly 1 time ---- 151355713 pairs aligned 0 times concordantly or discordantly; of these: 302711426 mates make up the pairs; of these: 300384501 (99.23%) aligned 0 times 620246 (0.20%) aligned exactly 1 time 1706679 (0.56%) aligned >1 times 6.12% overall alignment rate Time searching: 00:57:41 Overall time: 00:57:41 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] 3820972 / 8534705 = 0.4477 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 07:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.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 07:42:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:42:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:23: 1000000 INFO @ Sat, 03 Apr 2021 07:42:32: 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 07:42:42: 3000000 INFO @ Sat, 03 Apr 2021 07:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.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 07:42:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:42:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:52: 4000000 INFO @ Sat, 03 Apr 2021 07:42:53: 1000000 INFO @ Sat, 03 Apr 2021 07:43:02: 5000000 INFO @ Sat, 03 Apr 2021 07:43:04: 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 07:43:12: 6000000 INFO @ Sat, 03 Apr 2021 07:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.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 07:43:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:43:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:43:14: 3000000 INFO @ Sat, 03 Apr 2021 07:43:22: 7000000 INFO @ Sat, 03 Apr 2021 07:43:25: 4000000 INFO @ Sat, 03 Apr 2021 07:43:27: 1000000 INFO @ Sat, 03 Apr 2021 07:43:31: 8000000 INFO @ Sat, 03 Apr 2021 07:43:36: 5000000 INFO @ Sat, 03 Apr 2021 07:43:40: 2000000 INFO @ Sat, 03 Apr 2021 07:43:41: 9000000 INFO @ Sat, 03 Apr 2021 07:43:46: 6000000 INFO @ Sat, 03 Apr 2021 07:43:51: 10000000 INFO @ Sat, 03 Apr 2021 07:43:54: 3000000 INFO @ Sat, 03 Apr 2021 07:43:57: 7000000 INFO @ Sat, 03 Apr 2021 07:44:02: 11000000 INFO @ Sat, 03 Apr 2021 07:44:07: 8000000 INFO @ Sat, 03 Apr 2021 07:44:07: 4000000 INFO @ Sat, 03 Apr 2021 07:44:11: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:44:11: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:44:11: #1 total tags in treatment: 4075634 INFO @ Sat, 03 Apr 2021 07:44:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:44:11: #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 07:44:11: #1 tags after filtering in treatment: 2985484 INFO @ Sat, 03 Apr 2021 07:44:11: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:44:11: #1 finished! INFO @ Sat, 03 Apr 2021 07:44:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:44:11: #2 number of paired peaks: 2150 INFO @ Sat, 03 Apr 2021 07:44:11: start model_add_line... INFO @ Sat, 03 Apr 2021 07:44:11: start X-correlation... INFO @ Sat, 03 Apr 2021 07:44:11: end of X-cor INFO @ Sat, 03 Apr 2021 07:44:11: #2 finished! INFO @ Sat, 03 Apr 2021 07:44:11: #2 predicted fragment length is 143 bps INFO @ Sat, 03 Apr 2021 07:44:11: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 03 Apr 2021 07:44:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.05_model.r WARNING @ Sat, 03 Apr 2021 07:44:11: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:44:11: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 03 Apr 2021 07:44:11: #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 07:44:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:44:18: 9000000 INFO @ Sat, 03 Apr 2021 07:44:20: 5000000 INFO @ Sat, 03 Apr 2021 07:44:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.05_summits.bed INFO @ Sat, 03 Apr 2021 07:44:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3639 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:44:28: 10000000 INFO @ Sat, 03 Apr 2021 07:44:34: 6000000 INFO @ Sat, 03 Apr 2021 07:44:39: 11000000 INFO @ Sat, 03 Apr 2021 07:44:46: 7000000 INFO @ Sat, 03 Apr 2021 07:44:48: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:44:48: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:44:48: #1 total tags in treatment: 4075634 INFO @ Sat, 03 Apr 2021 07:44:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:44:48: #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 07:44:48: #1 tags after filtering in treatment: 2985484 INFO @ Sat, 03 Apr 2021 07:44:48: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:44:48: #1 finished! INFO @ Sat, 03 Apr 2021 07:44:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:44:49: #2 number of paired peaks: 2150 INFO @ Sat, 03 Apr 2021 07:44:49: start model_add_line... INFO @ Sat, 03 Apr 2021 07:44:49: start X-correlation... INFO @ Sat, 03 Apr 2021 07:44:49: end of X-cor INFO @ Sat, 03 Apr 2021 07:44:49: #2 finished! INFO @ Sat, 03 Apr 2021 07:44:49: #2 predicted fragment length is 143 bps INFO @ Sat, 03 Apr 2021 07:44:49: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 03 Apr 2021 07:44:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.10_model.r WARNING @ Sat, 03 Apr 2021 07:44:49: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:44:49: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 03 Apr 2021 07:44:49: #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 07:44:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:44:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:44:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:44:59: 8000000 INFO @ Sat, 03 Apr 2021 07:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.10_summits.bed INFO @ Sat, 03 Apr 2021 07:45:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1464 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:45:11: 9000000 INFO @ Sat, 03 Apr 2021 07:45:23: 10000000 INFO @ Sat, 03 Apr 2021 07:45:36: 11000000 INFO @ Sat, 03 Apr 2021 07:45:47: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:45:47: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:45:47: #1 total tags in treatment: 4075634 INFO @ Sat, 03 Apr 2021 07:45:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:45:47: #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 07:45:47: #1 tags after filtering in treatment: 2985484 INFO @ Sat, 03 Apr 2021 07:45:47: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:45:47: #1 finished! INFO @ Sat, 03 Apr 2021 07:45:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:45:47: #2 number of paired peaks: 2150 INFO @ Sat, 03 Apr 2021 07:45:47: start model_add_line... INFO @ Sat, 03 Apr 2021 07:45:47: start X-correlation... INFO @ Sat, 03 Apr 2021 07:45:47: end of X-cor INFO @ Sat, 03 Apr 2021 07:45:47: #2 finished! INFO @ Sat, 03 Apr 2021 07:45:47: #2 predicted fragment length is 143 bps INFO @ Sat, 03 Apr 2021 07:45:47: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 03 Apr 2021 07:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.20_model.r WARNING @ Sat, 03 Apr 2021 07:45:47: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:45:47: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 03 Apr 2021 07:45:47: #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 07:45:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:45:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:46:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:46:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:46:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2789125/SRX2789125.20_summits.bed INFO @ Sat, 03 Apr 2021 07:46:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (516 records, 4 fields): 4 millis CompletedMACS2peakCalling