Job ID = 14171785 SRX = SRX9008834 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10890157 spots for SRR12518306/SRR12518306.sra Written 10890157 spots for SRR12518306/SRR12518306.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172295 ("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: 00:22:30 10890157 reads; of these: 10890157 (100.00%) were paired; of these: 2086077 (19.16%) aligned concordantly 0 times 6937518 (63.70%) aligned concordantly exactly 1 time 1866562 (17.14%) aligned concordantly >1 times ---- 2086077 pairs aligned concordantly 0 times; of these: 608001 (29.15%) aligned discordantly 1 time ---- 1478076 pairs aligned 0 times concordantly or discordantly; of these: 2956152 mates make up the pairs; of these: 2413325 (81.64%) aligned 0 times 215188 (7.28%) aligned exactly 1 time 327639 (11.08%) aligned >1 times 88.92% overall alignment rate Time searching: 00:22:30 Overall time: 00:22:30 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] 917309 / 9349151 = 0.0981 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 13:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.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 13:18:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:18:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:18:45: 1000000 INFO @ Sat, 11 Dec 2021 13:18:50: 2000000 INFO @ Sat, 11 Dec 2021 13:18:56: 3000000 INFO @ Sat, 11 Dec 2021 13:19:01: 4000000 INFO @ Sat, 11 Dec 2021 13:19:07: 5000000 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 13:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.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 13:19:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:19:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:19:12: 6000000 INFO @ Sat, 11 Dec 2021 13:19:15: 1000000 INFO @ Sat, 11 Dec 2021 13:19:19: 7000000 INFO @ Sat, 11 Dec 2021 13:19:21: 2000000 INFO @ Sat, 11 Dec 2021 13:19:25: 8000000 INFO @ Sat, 11 Dec 2021 13:19:28: 3000000 INFO @ Sat, 11 Dec 2021 13:19:31: 9000000 INFO @ Sat, 11 Dec 2021 13:19:34: 4000000 INFO @ Sat, 11 Dec 2021 13:19:37: 10000000 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 13:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.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 13:19:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:19:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:19:40: 5000000 INFO @ Sat, 11 Dec 2021 13:19:43: 11000000 INFO @ Sat, 11 Dec 2021 13:19:45: 1000000 INFO @ Sat, 11 Dec 2021 13:19:46: 6000000 INFO @ Sat, 11 Dec 2021 13:19:49: 12000000 INFO @ Sat, 11 Dec 2021 13:19:52: 2000000 INFO @ Sat, 11 Dec 2021 13:19:52: 7000000 INFO @ Sat, 11 Dec 2021 13:19:55: 13000000 INFO @ Sat, 11 Dec 2021 13:19:58: 3000000 INFO @ Sat, 11 Dec 2021 13:19:58: 8000000 INFO @ Sat, 11 Dec 2021 13:20:02: 14000000 INFO @ Sat, 11 Dec 2021 13:20:04: 4000000 INFO @ Sat, 11 Dec 2021 13:20:05: 9000000 INFO @ Sat, 11 Dec 2021 13:20:08: 15000000 INFO @ Sat, 11 Dec 2021 13:20:10: 5000000 INFO @ Sat, 11 Dec 2021 13:20:11: 10000000 INFO @ Sat, 11 Dec 2021 13:20:14: 16000000 INFO @ Sat, 11 Dec 2021 13:20:17: 6000000 INFO @ Sat, 11 Dec 2021 13:20:17: 11000000 INFO @ Sat, 11 Dec 2021 13:20:20: 17000000 INFO @ Sat, 11 Dec 2021 13:20:23: 7000000 INFO @ Sat, 11 Dec 2021 13:20:23: 12000000 INFO @ Sat, 11 Dec 2021 13:20:23: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:20:23: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:20:23: #1 total tags in treatment: 7925082 INFO @ Sat, 11 Dec 2021 13:20:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:20:23: #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 13:20:24: #1 tags after filtering in treatment: 7730539 INFO @ Sat, 11 Dec 2021 13:20:24: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 13:20:24: #1 finished! INFO @ Sat, 11 Dec 2021 13:20:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:20:24: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 13:20:24: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 13:20:24: start model_add_line... INFO @ Sat, 11 Dec 2021 13:20:24: start X-correlation... INFO @ Sat, 11 Dec 2021 13:20:24: end of X-cor INFO @ Sat, 11 Dec 2021 13:20:24: #2 finished! INFO @ Sat, 11 Dec 2021 13:20:24: #2 predicted fragment length is 180 bps INFO @ Sat, 11 Dec 2021 13:20:24: #2 alternative fragment length(s) may be 180,196 bps INFO @ Sat, 11 Dec 2021 13:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.05_model.r WARNING @ Sat, 11 Dec 2021 13:20:24: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:20:24: #2 You may need to consider one of the other alternative d(s): 180,196 WARNING @ Sat, 11 Dec 2021 13:20:24: #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 13:20:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:20:29: 8000000 INFO @ Sat, 11 Dec 2021 13:20:29: 13000000 INFO @ Sat, 11 Dec 2021 13:20:35: 9000000 INFO @ Sat, 11 Dec 2021 13:20:36: 14000000 INFO @ Sat, 11 Dec 2021 13:20:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:20:41: 10000000 INFO @ Sat, 11 Dec 2021 13:20:42: 15000000 INFO @ Sat, 11 Dec 2021 13:20:47: 11000000 INFO @ Sat, 11 Dec 2021 13:20:48: 16000000 INFO @ Sat, 11 Dec 2021 13:20:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:20:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:20:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.05_summits.bed INFO @ Sat, 11 Dec 2021 13:20:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (686 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:20:54: 12000000 INFO @ Sat, 11 Dec 2021 13:20:54: 17000000 INFO @ Sat, 11 Dec 2021 13:20:57: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:20:57: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:20:57: #1 total tags in treatment: 7925082 INFO @ Sat, 11 Dec 2021 13:20:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:20:57: #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 13:20:58: #1 tags after filtering in treatment: 7730539 INFO @ Sat, 11 Dec 2021 13:20:58: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 13:20:58: #1 finished! INFO @ Sat, 11 Dec 2021 13:20:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:20:58: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 13:20:58: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 13:20:58: start model_add_line... INFO @ Sat, 11 Dec 2021 13:20:58: start X-correlation... INFO @ Sat, 11 Dec 2021 13:20:58: end of X-cor INFO @ Sat, 11 Dec 2021 13:20:58: #2 finished! INFO @ Sat, 11 Dec 2021 13:20:58: #2 predicted fragment length is 180 bps INFO @ Sat, 11 Dec 2021 13:20:58: #2 alternative fragment length(s) may be 180,196 bps INFO @ Sat, 11 Dec 2021 13:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.10_model.r WARNING @ Sat, 11 Dec 2021 13:20:58: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:20:58: #2 You may need to consider one of the other alternative d(s): 180,196 WARNING @ Sat, 11 Dec 2021 13:20:58: #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 13:20:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:21:00: 13000000 INFO @ Sat, 11 Dec 2021 13:21:05: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:21:11: 15000000 INFO @ Sat, 11 Dec 2021 13:21:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:21:17: 16000000 INFO @ Sat, 11 Dec 2021 13:21:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:21:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:21:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.10_summits.bed INFO @ Sat, 11 Dec 2021 13:21:22: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:21:23: 17000000 INFO @ Sat, 11 Dec 2021 13:21:26: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:21:26: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:21:26: #1 total tags in treatment: 7925082 INFO @ Sat, 11 Dec 2021 13:21:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:21:26: #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 13:21:26: #1 tags after filtering in treatment: 7730539 INFO @ Sat, 11 Dec 2021 13:21:26: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 13:21:26: #1 finished! INFO @ Sat, 11 Dec 2021 13:21:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:21:27: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 13:21:27: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 13:21:27: start model_add_line... INFO @ Sat, 11 Dec 2021 13:21:27: start X-correlation... INFO @ Sat, 11 Dec 2021 13:21:27: end of X-cor INFO @ Sat, 11 Dec 2021 13:21:27: #2 finished! INFO @ Sat, 11 Dec 2021 13:21:27: #2 predicted fragment length is 180 bps INFO @ Sat, 11 Dec 2021 13:21:27: #2 alternative fragment length(s) may be 180,196 bps INFO @ Sat, 11 Dec 2021 13:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.20_model.r WARNING @ Sat, 11 Dec 2021 13:21:27: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:21:27: #2 You may need to consider one of the other alternative d(s): 180,196 WARNING @ Sat, 11 Dec 2021 13:21:27: #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 13:21:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:21:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008834/SRX9008834.20_summits.bed INFO @ Sat, 11 Dec 2021 13:21:50: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (100 records, 4 fields): 2 millis CompletedMACS2peakCalling