Job ID = 12265352 SRX = SRX6430368 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16541123 spots for SRR9669873/SRR9669873.sra Written 16541123 spots for SRR9669873/SRR9669873.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265510 ("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: 00:10:56 16541123 reads; of these: 16541123 (100.00%) were paired; of these: 9602253 (58.05%) aligned concordantly 0 times 4784196 (28.92%) aligned concordantly exactly 1 time 2154674 (13.03%) aligned concordantly >1 times ---- 9602253 pairs aligned concordantly 0 times; of these: 1021691 (10.64%) aligned discordantly 1 time ---- 8580562 pairs aligned 0 times concordantly or discordantly; of these: 17161124 mates make up the pairs; of these: 16277313 (94.85%) aligned 0 times 336311 (1.96%) aligned exactly 1 time 547500 (3.19%) aligned >1 times 50.80% overall alignment rate Time searching: 00:10:56 Overall time: 00:10:56 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] 989475 / 7836537 = 0.1263 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 06:56:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.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 06:56:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:56:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:56:31: 1000000 INFO @ Sat, 03 Apr 2021 06:56:39: 2000000 INFO @ Sat, 03 Apr 2021 06:56:46: 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 06:56:53: 4000000 INFO @ Sat, 03 Apr 2021 06:56:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.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 06:56:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:56:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:01: 5000000 INFO @ Sat, 03 Apr 2021 06:57:01: 1000000 INFO @ Sat, 03 Apr 2021 06:57:08: 6000000 INFO @ Sat, 03 Apr 2021 06:57:08: 2000000 INFO @ Sat, 03 Apr 2021 06:57:15: 7000000 INFO @ Sat, 03 Apr 2021 06:57:15: 3000000 INFO @ Sat, 03 Apr 2021 06:57:22: 4000000 INFO @ Sat, 03 Apr 2021 06:57:22: 8000000 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 06:57:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.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 06:57:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:29: 5000000 INFO @ Sat, 03 Apr 2021 06:57:29: 9000000 INFO @ Sat, 03 Apr 2021 06:57:32: 1000000 INFO @ Sat, 03 Apr 2021 06:57:37: 6000000 INFO @ Sat, 03 Apr 2021 06:57:37: 10000000 INFO @ Sat, 03 Apr 2021 06:57:40: 2000000 INFO @ Sat, 03 Apr 2021 06:57:44: 7000000 INFO @ Sat, 03 Apr 2021 06:57:44: 11000000 INFO @ Sat, 03 Apr 2021 06:57:48: 3000000 INFO @ Sat, 03 Apr 2021 06:57:52: 8000000 INFO @ Sat, 03 Apr 2021 06:57:52: 12000000 INFO @ Sat, 03 Apr 2021 06:57:55: 4000000 INFO @ Sat, 03 Apr 2021 06:58:00: 9000000 INFO @ Sat, 03 Apr 2021 06:58:00: 13000000 INFO @ Sat, 03 Apr 2021 06:58:03: 5000000 INFO @ Sat, 03 Apr 2021 06:58:07: 10000000 INFO @ Sat, 03 Apr 2021 06:58:07: 14000000 INFO @ Sat, 03 Apr 2021 06:58:11: 6000000 INFO @ Sat, 03 Apr 2021 06:58:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:58:14: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:58:14: #1 total tags in treatment: 5994930 INFO @ Sat, 03 Apr 2021 06:58:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:58:14: #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 06:58:14: #1 tags after filtering in treatment: 5079616 INFO @ Sat, 03 Apr 2021 06:58:14: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 06:58:14: #1 finished! INFO @ Sat, 03 Apr 2021 06:58:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:58:14: #2 number of paired peaks: 403 WARNING @ Sat, 03 Apr 2021 06:58:14: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sat, 03 Apr 2021 06:58:14: start model_add_line... INFO @ Sat, 03 Apr 2021 06:58:14: start X-correlation... INFO @ Sat, 03 Apr 2021 06:58:14: end of X-cor INFO @ Sat, 03 Apr 2021 06:58:14: #2 finished! INFO @ Sat, 03 Apr 2021 06:58:14: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 06:58:14: #2 alternative fragment length(s) may be 4,86,517,554 bps INFO @ Sat, 03 Apr 2021 06:58:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.05_model.r WARNING @ Sat, 03 Apr 2021 06:58:14: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:58:14: #2 You may need to consider one of the other alternative d(s): 4,86,517,554 WARNING @ Sat, 03 Apr 2021 06:58:14: #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 06:58:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:58:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:58:14: 11000000 INFO @ Sat, 03 Apr 2021 06:58:19: 7000000 INFO @ Sat, 03 Apr 2021 06:58:22: 12000000 INFO @ Sat, 03 Apr 2021 06:58:27: 8000000 INFO @ Sat, 03 Apr 2021 06:58:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:58:29: 13000000 INFO @ Sat, 03 Apr 2021 06:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.05_summits.bed INFO @ Sat, 03 Apr 2021 06:58:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2988 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:58:35: 9000000 INFO @ Sat, 03 Apr 2021 06:58:37: 14000000 INFO @ Sat, 03 Apr 2021 06:58:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:58:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:58:43: #1 total tags in treatment: 5994930 INFO @ Sat, 03 Apr 2021 06:58:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:58:43: #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 06:58:43: #1 tags after filtering in treatment: 5079616 INFO @ Sat, 03 Apr 2021 06:58:43: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 06:58:43: #1 finished! INFO @ Sat, 03 Apr 2021 06:58:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:58:43: 10000000 INFO @ Sat, 03 Apr 2021 06:58:43: #2 number of paired peaks: 403 WARNING @ Sat, 03 Apr 2021 06:58:43: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sat, 03 Apr 2021 06:58:43: start model_add_line... INFO @ Sat, 03 Apr 2021 06:58:43: start X-correlation... INFO @ Sat, 03 Apr 2021 06:58:43: end of X-cor INFO @ Sat, 03 Apr 2021 06:58:43: #2 finished! INFO @ Sat, 03 Apr 2021 06:58:43: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 06:58:43: #2 alternative fragment length(s) may be 4,86,517,554 bps INFO @ Sat, 03 Apr 2021 06:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.10_model.r WARNING @ Sat, 03 Apr 2021 06:58:43: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:58:43: #2 You may need to consider one of the other alternative d(s): 4,86,517,554 WARNING @ Sat, 03 Apr 2021 06:58:43: #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 06:58:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:58:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:58:50: 11000000 INFO @ Sat, 03 Apr 2021 06:58:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:58:58: 12000000 INFO @ Sat, 03 Apr 2021 06:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.10_summits.bed INFO @ Sat, 03 Apr 2021 06:59:03: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (813 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:59:05: 13000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:59:12: 14000000 INFO @ Sat, 03 Apr 2021 06:59:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:59:18: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:59:18: #1 total tags in treatment: 5994930 INFO @ Sat, 03 Apr 2021 06:59:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:18: #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 06:59:18: #1 tags after filtering in treatment: 5079616 INFO @ Sat, 03 Apr 2021 06:59:18: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 06:59:18: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:18: #2 number of paired peaks: 403 WARNING @ Sat, 03 Apr 2021 06:59:18: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sat, 03 Apr 2021 06:59:18: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:18: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:18: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:18: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:18: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 06:59:18: #2 alternative fragment length(s) may be 4,86,517,554 bps INFO @ Sat, 03 Apr 2021 06:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.20_model.r WARNING @ Sat, 03 Apr 2021 06:59:18: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:59:18: #2 You may need to consider one of the other alternative d(s): 4,86,517,554 WARNING @ Sat, 03 Apr 2021 06:59:18: #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 06:59:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:59:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:59:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430368/SRX6430368.20_summits.bed INFO @ Sat, 03 Apr 2021 06:59:37: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 2 millis CompletedMACS2peakCalling