Job ID = 14171531 SRX = SRX10386206 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18415433 spots for SRR14009271/SRR14009271.sra Written 18415433 spots for SRR14009271/SRR14009271.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172127 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:38:08 18415433 reads; of these: 18415433 (100.00%) were paired; of these: 5982489 (32.49%) aligned concordantly 0 times 8633904 (46.88%) aligned concordantly exactly 1 time 3799040 (20.63%) aligned concordantly >1 times ---- 5982489 pairs aligned concordantly 0 times; of these: 304372 (5.09%) aligned discordantly 1 time ---- 5678117 pairs aligned 0 times concordantly or discordantly; of these: 11356234 mates make up the pairs; of these: 10547231 (92.88%) aligned 0 times 382253 (3.37%) aligned exactly 1 time 426750 (3.76%) aligned >1 times 71.36% overall alignment rate Time searching: 00:38:09 Overall time: 00:38:09 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] 1702851 / 12672529 = 0.1344 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 12:43:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.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 12:43:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:43:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:43:56: 1000000 INFO @ Sat, 11 Dec 2021 12:44:01: 2000000 INFO @ Sat, 11 Dec 2021 12:44:08: 3000000 INFO @ Sat, 11 Dec 2021 12:44:14: 4000000 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 12:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.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 12:44:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:44:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:44:20: 5000000 INFO @ Sat, 11 Dec 2021 12:44:26: 1000000 INFO @ Sat, 11 Dec 2021 12:44:26: 6000000 INFO @ Sat, 11 Dec 2021 12:44:32: 2000000 INFO @ Sat, 11 Dec 2021 12:44:32: 7000000 INFO @ Sat, 11 Dec 2021 12:44:38: 3000000 INFO @ Sat, 11 Dec 2021 12:44:38: 8000000 INFO @ Sat, 11 Dec 2021 12:44:44: 9000000 INFO @ Sat, 11 Dec 2021 12:44:44: 4000000 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 12:44:50: 10000000 INFO @ Sat, 11 Dec 2021 12:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.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 12:44:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:44:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:44:50: 5000000 INFO @ Sat, 11 Dec 2021 12:44:56: 11000000 INFO @ Sat, 11 Dec 2021 12:44:56: 6000000 INFO @ Sat, 11 Dec 2021 12:44:56: 1000000 INFO @ Sat, 11 Dec 2021 12:45:02: 12000000 INFO @ Sat, 11 Dec 2021 12:45:03: 7000000 INFO @ Sat, 11 Dec 2021 12:45:03: 2000000 INFO @ Sat, 11 Dec 2021 12:45:08: 13000000 INFO @ Sat, 11 Dec 2021 12:45:09: 8000000 INFO @ Sat, 11 Dec 2021 12:45:09: 3000000 INFO @ Sat, 11 Dec 2021 12:45:14: 14000000 INFO @ Sat, 11 Dec 2021 12:45:15: 9000000 INFO @ Sat, 11 Dec 2021 12:45:16: 4000000 INFO @ Sat, 11 Dec 2021 12:45:21: 15000000 INFO @ Sat, 11 Dec 2021 12:45:21: 10000000 INFO @ Sat, 11 Dec 2021 12:45:22: 5000000 INFO @ Sat, 11 Dec 2021 12:45:27: 16000000 INFO @ Sat, 11 Dec 2021 12:45:28: 11000000 INFO @ Sat, 11 Dec 2021 12:45:29: 6000000 INFO @ Sat, 11 Dec 2021 12:45:33: 17000000 INFO @ Sat, 11 Dec 2021 12:45:34: 12000000 INFO @ Sat, 11 Dec 2021 12:45:35: 7000000 INFO @ Sat, 11 Dec 2021 12:45:39: 18000000 INFO @ Sat, 11 Dec 2021 12:45:41: 13000000 INFO @ Sat, 11 Dec 2021 12:45:42: 8000000 INFO @ Sat, 11 Dec 2021 12:45:45: 19000000 INFO @ Sat, 11 Dec 2021 12:45:47: 14000000 INFO @ Sat, 11 Dec 2021 12:45:49: 9000000 INFO @ Sat, 11 Dec 2021 12:45:51: 20000000 INFO @ Sat, 11 Dec 2021 12:45:53: 15000000 INFO @ Sat, 11 Dec 2021 12:45:55: 10000000 INFO @ Sat, 11 Dec 2021 12:45:58: 21000000 INFO @ Sat, 11 Dec 2021 12:45:59: 16000000 INFO @ Sat, 11 Dec 2021 12:46:02: 11000000 INFO @ Sat, 11 Dec 2021 12:46:04: 22000000 INFO @ Sat, 11 Dec 2021 12:46:05: 17000000 INFO @ Sat, 11 Dec 2021 12:46:09: 12000000 INFO @ Sat, 11 Dec 2021 12:46:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:46:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:46:09: #1 total tags in treatment: 10772764 INFO @ Sat, 11 Dec 2021 12:46:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:46:09: #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 12:46:10: #1 tags after filtering in treatment: 9660718 INFO @ Sat, 11 Dec 2021 12:46:10: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 12:46:10: #1 finished! INFO @ Sat, 11 Dec 2021 12:46:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:46:10: #2 number of paired peaks: 137 WARNING @ Sat, 11 Dec 2021 12:46:10: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 11 Dec 2021 12:46:10: start model_add_line... INFO @ Sat, 11 Dec 2021 12:46:10: start X-correlation... INFO @ Sat, 11 Dec 2021 12:46:10: end of X-cor INFO @ Sat, 11 Dec 2021 12:46:10: #2 finished! INFO @ Sat, 11 Dec 2021 12:46:10: #2 predicted fragment length is 99 bps INFO @ Sat, 11 Dec 2021 12:46:10: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 11 Dec 2021 12:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.05_model.r WARNING @ Sat, 11 Dec 2021 12:46:10: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:46:10: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 11 Dec 2021 12:46:10: #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 12:46:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:46:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:46:11: 18000000 INFO @ Sat, 11 Dec 2021 12:46:15: 13000000 INFO @ Sat, 11 Dec 2021 12:46:16: 19000000 INFO @ Sat, 11 Dec 2021 12:46:22: 14000000 INFO @ Sat, 11 Dec 2021 12:46:22: 20000000 INFO @ Sat, 11 Dec 2021 12:46:28: 21000000 INFO @ Sat, 11 Dec 2021 12:46:28: 15000000 INFO @ Sat, 11 Dec 2021 12:46:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:46:34: 22000000 INFO @ Sat, 11 Dec 2021 12:46:35: 16000000 INFO @ Sat, 11 Dec 2021 12:46:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:46:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:46:39: #1 total tags in treatment: 10772764 INFO @ Sat, 11 Dec 2021 12:46:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:46:39: #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 12:46:39: #1 tags after filtering in treatment: 9660718 INFO @ Sat, 11 Dec 2021 12:46:39: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 12:46:39: #1 finished! INFO @ Sat, 11 Dec 2021 12:46:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:46:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:46:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:46:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.05_summits.bed INFO @ Sat, 11 Dec 2021 12:46:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1177 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:46:40: #2 number of paired peaks: 137 WARNING @ Sat, 11 Dec 2021 12:46:40: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 11 Dec 2021 12:46:40: start model_add_line... INFO @ Sat, 11 Dec 2021 12:46:40: start X-correlation... INFO @ Sat, 11 Dec 2021 12:46:40: end of X-cor INFO @ Sat, 11 Dec 2021 12:46:40: #2 finished! INFO @ Sat, 11 Dec 2021 12:46:40: #2 predicted fragment length is 99 bps INFO @ Sat, 11 Dec 2021 12:46:40: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 11 Dec 2021 12:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.10_model.r WARNING @ Sat, 11 Dec 2021 12:46:40: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:46:40: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 11 Dec 2021 12:46:40: #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 12:46:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:46:42: 17000000 INFO @ Sat, 11 Dec 2021 12:46:49: 18000000 INFO @ Sat, 11 Dec 2021 12:46:56: 19000000 INFO @ Sat, 11 Dec 2021 12:46:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:47:03: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.10_summits.bed INFO @ Sat, 11 Dec 2021 12:47:09: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (743 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:47:10: 21000000 INFO @ Sat, 11 Dec 2021 12:47:16: 22000000 INFO @ Sat, 11 Dec 2021 12:47:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:47:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:47:22: #1 total tags in treatment: 10772764 INFO @ Sat, 11 Dec 2021 12:47:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:47:22: #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 12:47:22: #1 tags after filtering in treatment: 9660718 INFO @ Sat, 11 Dec 2021 12:47:22: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 12:47:22: #1 finished! INFO @ Sat, 11 Dec 2021 12:47:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:47:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:47:23: #2 number of paired peaks: 137 WARNING @ Sat, 11 Dec 2021 12:47:23: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 11 Dec 2021 12:47:23: start model_add_line... INFO @ Sat, 11 Dec 2021 12:47:23: start X-correlation... INFO @ Sat, 11 Dec 2021 12:47:23: end of X-cor INFO @ Sat, 11 Dec 2021 12:47:23: #2 finished! INFO @ Sat, 11 Dec 2021 12:47:23: #2 predicted fragment length is 99 bps INFO @ Sat, 11 Dec 2021 12:47:23: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 11 Dec 2021 12:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.20_model.r WARNING @ Sat, 11 Dec 2021 12:47:23: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:47:23: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 11 Dec 2021 12:47:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:47:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:47:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386206/SRX10386206.20_summits.bed INFO @ Sat, 11 Dec 2021 12:47:52: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (407 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。