Job ID = 14172166 SRX = SRX9786720 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14637160 spots for SRR13362639/SRR13362639.sra Written 14637160 spots for SRR13362639/SRR13362639.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172681 ("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: 00:16:27 14637160 reads; of these: 14637160 (100.00%) were paired; of these: 2760114 (18.86%) aligned concordantly 0 times 7579512 (51.78%) aligned concordantly exactly 1 time 4297534 (29.36%) aligned concordantly >1 times ---- 2760114 pairs aligned concordantly 0 times; of these: 1020657 (36.98%) aligned discordantly 1 time ---- 1739457 pairs aligned 0 times concordantly or discordantly; of these: 3478914 mates make up the pairs; of these: 2332387 (67.04%) aligned 0 times 469453 (13.49%) aligned exactly 1 time 677074 (19.46%) aligned >1 times 92.03% overall alignment rate Time searching: 00:16:27 Overall time: 00:16:27 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] 2797196 / 12783950 = 0.2188 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 15:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.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 15:00:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:07: 1000000 INFO @ Sat, 11 Dec 2021 15:00:13: 2000000 INFO @ Sat, 11 Dec 2021 15:00:19: 3000000 INFO @ Sat, 11 Dec 2021 15:00:25: 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 15:00:30: 5000000 INFO @ Sat, 11 Dec 2021 15:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.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 15:00:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:36: 6000000 INFO @ Sat, 11 Dec 2021 15:00:38: 1000000 INFO @ Sat, 11 Dec 2021 15:00:42: 7000000 INFO @ Sat, 11 Dec 2021 15:00:45: 2000000 INFO @ Sat, 11 Dec 2021 15:00:48: 8000000 INFO @ Sat, 11 Dec 2021 15:00:52: 3000000 INFO @ Sat, 11 Dec 2021 15:00:55: 9000000 INFO @ Sat, 11 Dec 2021 15:00:59: 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 15:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.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 15:01:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:01:01: 10000000 INFO @ Sat, 11 Dec 2021 15:01:06: 5000000 INFO @ Sat, 11 Dec 2021 15:01:07: 11000000 INFO @ Sat, 11 Dec 2021 15:01:07: 1000000 INFO @ Sat, 11 Dec 2021 15:01:13: 6000000 INFO @ Sat, 11 Dec 2021 15:01:13: 12000000 INFO @ Sat, 11 Dec 2021 15:01:14: 2000000 INFO @ Sat, 11 Dec 2021 15:01:19: 13000000 INFO @ Sat, 11 Dec 2021 15:01:20: 7000000 INFO @ Sat, 11 Dec 2021 15:01:20: 3000000 INFO @ Sat, 11 Dec 2021 15:01:26: 14000000 INFO @ Sat, 11 Dec 2021 15:01:26: 4000000 INFO @ Sat, 11 Dec 2021 15:01:27: 8000000 INFO @ Sat, 11 Dec 2021 15:01:32: 15000000 INFO @ Sat, 11 Dec 2021 15:01:32: 5000000 INFO @ Sat, 11 Dec 2021 15:01:34: 9000000 INFO @ Sat, 11 Dec 2021 15:01:38: 16000000 INFO @ Sat, 11 Dec 2021 15:01:39: 6000000 INFO @ Sat, 11 Dec 2021 15:01:41: 10000000 INFO @ Sat, 11 Dec 2021 15:01:44: 17000000 INFO @ Sat, 11 Dec 2021 15:01:45: 7000000 INFO @ Sat, 11 Dec 2021 15:01:48: 11000000 INFO @ Sat, 11 Dec 2021 15:01:50: 18000000 INFO @ Sat, 11 Dec 2021 15:01:51: 8000000 INFO @ Sat, 11 Dec 2021 15:01:55: 12000000 INFO @ Sat, 11 Dec 2021 15:01:57: 19000000 INFO @ Sat, 11 Dec 2021 15:01:57: 9000000 INFO @ Sat, 11 Dec 2021 15:02:02: 13000000 INFO @ Sat, 11 Dec 2021 15:02:03: 20000000 INFO @ Sat, 11 Dec 2021 15:02:03: 10000000 INFO @ Sat, 11 Dec 2021 15:02:09: 21000000 INFO @ Sat, 11 Dec 2021 15:02:09: 14000000 INFO @ Sat, 11 Dec 2021 15:02:10: 11000000 INFO @ Sat, 11 Dec 2021 15:02:11: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:02:11: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:02:11: #1 total tags in treatment: 9145034 INFO @ Sat, 11 Dec 2021 15:02:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:11: #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 15:02:11: #1 tags after filtering in treatment: 7406550 INFO @ Sat, 11 Dec 2021 15:02:11: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 11 Dec 2021 15:02:11: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:12: #2 number of paired peaks: 751 WARNING @ Sat, 11 Dec 2021 15:02:12: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sat, 11 Dec 2021 15:02:12: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:12: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:12: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:12: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:12: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 15:02:12: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 15:02:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.05_model.r WARNING @ Sat, 11 Dec 2021 15:02:12: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:02:12: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 15:02:12: #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 15:02:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:02:16: 12000000 INFO @ Sat, 11 Dec 2021 15:02:16: 15000000 INFO @ Sat, 11 Dec 2021 15:02:22: 13000000 INFO @ Sat, 11 Dec 2021 15:02:23: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:02:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:02:28: 14000000 INFO @ Sat, 11 Dec 2021 15:02:30: 17000000 INFO @ Sat, 11 Dec 2021 15:02:34: 15000000 INFO @ Sat, 11 Dec 2021 15:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.05_summits.bed INFO @ Sat, 11 Dec 2021 15:02:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5364 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:02:37: 18000000 INFO @ Sat, 11 Dec 2021 15:02:40: 16000000 INFO @ Sat, 11 Dec 2021 15:02:44: 19000000 INFO @ Sat, 11 Dec 2021 15:02:46: 17000000 INFO @ Sat, 11 Dec 2021 15:02:51: 20000000 INFO @ Sat, 11 Dec 2021 15:02:53: 18000000 INFO @ Sat, 11 Dec 2021 15:02:58: 21000000 INFO @ Sat, 11 Dec 2021 15:02:59: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:03:01: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:03:01: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:03:01: #1 total tags in treatment: 9145034 INFO @ Sat, 11 Dec 2021 15:03:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:01: #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 15:03:01: #1 tags after filtering in treatment: 7406550 INFO @ Sat, 11 Dec 2021 15:03:01: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 11 Dec 2021 15:03:01: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:02: #2 number of paired peaks: 751 WARNING @ Sat, 11 Dec 2021 15:03:02: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sat, 11 Dec 2021 15:03:02: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:02: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:02: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:02: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:02: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 15:03:02: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 15:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.10_model.r WARNING @ Sat, 11 Dec 2021 15:03:02: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:03:02: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 15:03:02: #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 15:03:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:03:05: 20000000 INFO @ Sat, 11 Dec 2021 15:03:10: 21000000 INFO @ Sat, 11 Dec 2021 15:03:12: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:03:12: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:03:12: #1 total tags in treatment: 9145034 INFO @ Sat, 11 Dec 2021 15:03:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:12: #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 15:03:12: #1 tags after filtering in treatment: 7406550 INFO @ Sat, 11 Dec 2021 15:03:12: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 11 Dec 2021 15:03:12: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:13: #2 number of paired peaks: 751 WARNING @ Sat, 11 Dec 2021 15:03:13: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sat, 11 Dec 2021 15:03:13: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:13: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:13: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:13: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:13: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 15:03:13: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 15:03:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.20_model.r WARNING @ Sat, 11 Dec 2021 15:03:13: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:03:13: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 15:03:13: #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 15:03:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:03:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.10_summits.bed INFO @ Sat, 11 Dec 2021 15:03:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2241 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:03:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786720/SRX9786720.20_summits.bed INFO @ Sat, 11 Dec 2021 15:03:36: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (460 records, 4 fields): 13 millis CompletedMACS2peakCalling