Job ID = 14166951 SRX = SRX7541112 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16095802 spots for SRR10871158/SRR10871158.sra Written 16095802 spots for SRR10871158/SRR10871158.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167357 ("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: 00:42:22 16095802 reads; of these: 16095802 (100.00%) were paired; of these: 7378886 (45.84%) aligned concordantly 0 times 6811672 (42.32%) aligned concordantly exactly 1 time 1905244 (11.84%) aligned concordantly >1 times ---- 7378886 pairs aligned concordantly 0 times; of these: 1130630 (15.32%) aligned discordantly 1 time ---- 6248256 pairs aligned 0 times concordantly or discordantly; of these: 12496512 mates make up the pairs; of these: 10963652 (87.73%) aligned 0 times 625436 (5.00%) aligned exactly 1 time 907424 (7.26%) aligned >1 times 65.94% overall alignment rate Time searching: 00:42:22 Overall time: 00:42:22 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 12 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] 3995608 / 9834104 = 0.4063 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 @ Fri, 10 Dec 2021 08:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.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 @ Fri, 10 Dec 2021 08:59:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:59:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:59:33: 1000000 INFO @ Fri, 10 Dec 2021 08:59:41: 2000000 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 @ Fri, 10 Dec 2021 08:59:50: 3000000 INFO @ Fri, 10 Dec 2021 08:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.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 @ Fri, 10 Dec 2021 08:59:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:59:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:00:00: 4000000 INFO @ Fri, 10 Dec 2021 09:00:03: 1000000 INFO @ Fri, 10 Dec 2021 09:00:10: 5000000 INFO @ Fri, 10 Dec 2021 09:00:13: 2000000 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 @ Fri, 10 Dec 2021 09:00:20: 6000000 INFO @ Fri, 10 Dec 2021 09:00:23: 3000000 INFO @ Fri, 10 Dec 2021 09:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.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 @ Fri, 10 Dec 2021 09:00:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:00:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:00:29: 7000000 INFO @ Fri, 10 Dec 2021 09:00:33: 4000000 INFO @ Fri, 10 Dec 2021 09:00:35: 1000000 INFO @ Fri, 10 Dec 2021 09:00:39: 8000000 INFO @ Fri, 10 Dec 2021 09:00:43: 5000000 INFO @ Fri, 10 Dec 2021 09:00:45: 2000000 INFO @ Fri, 10 Dec 2021 09:00:49: 9000000 INFO @ Fri, 10 Dec 2021 09:00:57: 6000000 INFO @ Fri, 10 Dec 2021 09:01:00: 3000000 INFO @ Fri, 10 Dec 2021 09:01:03: 10000000 INFO @ Fri, 10 Dec 2021 09:01:07: 7000000 INFO @ Fri, 10 Dec 2021 09:01:10: 4000000 INFO @ Fri, 10 Dec 2021 09:01:14: 11000000 INFO @ Fri, 10 Dec 2021 09:01:17: 8000000 INFO @ Fri, 10 Dec 2021 09:01:20: 5000000 INFO @ Fri, 10 Dec 2021 09:01:23: 12000000 INFO @ Fri, 10 Dec 2021 09:01:27: 9000000 INFO @ Fri, 10 Dec 2021 09:01:30: 6000000 INFO @ Fri, 10 Dec 2021 09:01:33: 13000000 INFO @ Fri, 10 Dec 2021 09:01:36: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 09:01:36: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 09:01:36: #1 total tags in treatment: 4991878 INFO @ Fri, 10 Dec 2021 09:01:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:01:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:01:36: #1 tags after filtering in treatment: 4734991 INFO @ Fri, 10 Dec 2021 09:01:36: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 09:01:36: #1 finished! INFO @ Fri, 10 Dec 2021 09:01:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:01:36: #2 number of paired peaks: 494 WARNING @ Fri, 10 Dec 2021 09:01:36: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Fri, 10 Dec 2021 09:01:36: start model_add_line... INFO @ Fri, 10 Dec 2021 09:01:36: start X-correlation... INFO @ Fri, 10 Dec 2021 09:01:37: end of X-cor INFO @ Fri, 10 Dec 2021 09:01:37: #2 finished! INFO @ Fri, 10 Dec 2021 09:01:37: #2 predicted fragment length is 139 bps INFO @ Fri, 10 Dec 2021 09:01:37: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 10 Dec 2021 09:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.05_model.r WARNING @ Fri, 10 Dec 2021 09:01:37: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:01:37: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Fri, 10 Dec 2021 09:01:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:01:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:01:37: 10000000 INFO @ Fri, 10 Dec 2021 09:01:39: 7000000 INFO @ Fri, 10 Dec 2021 09:01:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:01:47: 11000000 INFO @ Fri, 10 Dec 2021 09:01:49: 8000000 INFO @ Fri, 10 Dec 2021 09:01:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.05_summits.bed INFO @ Fri, 10 Dec 2021 09:01:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1497 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:01:56: 12000000 INFO @ Fri, 10 Dec 2021 09:01:58: 9000000 INFO @ Fri, 10 Dec 2021 09:02:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:02:08: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 09:02:08: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 09:02:08: #1 total tags in treatment: 4991878 INFO @ Fri, 10 Dec 2021 09:02:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:02:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:02:08: 10000000 INFO @ Fri, 10 Dec 2021 09:02:08: #1 tags after filtering in treatment: 4734991 INFO @ Fri, 10 Dec 2021 09:02:08: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 09:02:08: #1 finished! INFO @ Fri, 10 Dec 2021 09:02:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:02:09: #2 number of paired peaks: 494 WARNING @ Fri, 10 Dec 2021 09:02:09: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Fri, 10 Dec 2021 09:02:09: start model_add_line... INFO @ Fri, 10 Dec 2021 09:02:09: start X-correlation... INFO @ Fri, 10 Dec 2021 09:02:09: end of X-cor INFO @ Fri, 10 Dec 2021 09:02:09: #2 finished! INFO @ Fri, 10 Dec 2021 09:02:09: #2 predicted fragment length is 139 bps INFO @ Fri, 10 Dec 2021 09:02:09: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 10 Dec 2021 09:02:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.10_model.r WARNING @ Fri, 10 Dec 2021 09:02:09: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:02:09: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Fri, 10 Dec 2021 09:02:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:02:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:02:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:02:17: 11000000 INFO @ Fri, 10 Dec 2021 09:02:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.10_summits.bed INFO @ Fri, 10 Dec 2021 09:02:24: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (731 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:02:26: 12000000 INFO @ Fri, 10 Dec 2021 09:02:35: 13000000 INFO @ Fri, 10 Dec 2021 09:02:37: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 09:02:37: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 09:02:37: #1 total tags in treatment: 4991878 INFO @ Fri, 10 Dec 2021 09:02:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:02:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:02:37: #1 tags after filtering in treatment: 4734991 INFO @ Fri, 10 Dec 2021 09:02:37: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 09:02:37: #1 finished! INFO @ Fri, 10 Dec 2021 09:02:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:02:37: #2 number of paired peaks: 494 WARNING @ Fri, 10 Dec 2021 09:02:37: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Fri, 10 Dec 2021 09:02:37: start model_add_line... INFO @ Fri, 10 Dec 2021 09:02:37: start X-correlation... INFO @ Fri, 10 Dec 2021 09:02:38: end of X-cor INFO @ Fri, 10 Dec 2021 09:02:38: #2 finished! INFO @ Fri, 10 Dec 2021 09:02:38: #2 predicted fragment length is 139 bps INFO @ Fri, 10 Dec 2021 09:02:38: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 10 Dec 2021 09:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.20_model.r WARNING @ Fri, 10 Dec 2021 09:02:38: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:02:38: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Fri, 10 Dec 2021 09:02:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:02:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:02:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:02:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541112/SRX7541112.20_summits.bed INFO @ Fri, 10 Dec 2021 09:02:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (384 records, 4 fields): 2 millis CompletedMACS2peakCalling