Job ID = 14170266 SRX = SRX10706038 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25113121 spots for SRR14352194/SRR14352194.sra Written 25113121 spots for SRR14352194/SRR14352194.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170928 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:05:59 25113121 reads; of these: 25113121 (100.00%) were paired; of these: 2013488 (8.02%) aligned concordantly 0 times 20216166 (80.50%) aligned concordantly exactly 1 time 2883467 (11.48%) aligned concordantly >1 times ---- 2013488 pairs aligned concordantly 0 times; of these: 336663 (16.72%) aligned discordantly 1 time ---- 1676825 pairs aligned 0 times concordantly or discordantly; of these: 3353650 mates make up the pairs; of these: 2183114 (65.10%) aligned 0 times 945460 (28.19%) aligned exactly 1 time 225076 (6.71%) aligned >1 times 95.65% overall alignment rate Time searching: 01:06:00 Overall time: 01:06:00 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 36 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] 6521843 / 20439359 = 0.3191 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 07:22:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.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 07:22:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:22:28: 1000000 INFO @ Sat, 11 Dec 2021 07:22:36: 2000000 INFO @ Sat, 11 Dec 2021 07:22:45: 3000000 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 07:22:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.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 07:22:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:22:55: 4000000 INFO @ Sat, 11 Dec 2021 07:22:58: 1000000 INFO @ Sat, 11 Dec 2021 07:23:05: 5000000 INFO @ Sat, 11 Dec 2021 07:23:08: 2000000 INFO @ Sat, 11 Dec 2021 07:23:14: 6000000 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 07:23:17: 3000000 INFO @ Sat, 11 Dec 2021 07:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.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 07:23:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:23:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:23:25: 7000000 INFO @ Sat, 11 Dec 2021 07:23:28: 4000000 INFO @ Sat, 11 Dec 2021 07:23:32: 1000000 INFO @ Sat, 11 Dec 2021 07:23:36: 8000000 INFO @ Sat, 11 Dec 2021 07:23:40: 5000000 INFO @ Sat, 11 Dec 2021 07:23:44: 2000000 INFO @ Sat, 11 Dec 2021 07:23:48: 9000000 INFO @ Sat, 11 Dec 2021 07:23:51: 6000000 INFO @ Sat, 11 Dec 2021 07:23:57: 3000000 INFO @ Sat, 11 Dec 2021 07:23:59: 10000000 INFO @ Sat, 11 Dec 2021 07:24:02: 7000000 INFO @ Sat, 11 Dec 2021 07:24:09: 4000000 INFO @ Sat, 11 Dec 2021 07:24:10: 11000000 INFO @ Sat, 11 Dec 2021 07:24:13: 8000000 INFO @ Sat, 11 Dec 2021 07:24:21: 12000000 INFO @ Sat, 11 Dec 2021 07:24:22: 5000000 INFO @ Sat, 11 Dec 2021 07:24:24: 9000000 INFO @ Sat, 11 Dec 2021 07:24:32: 13000000 INFO @ Sat, 11 Dec 2021 07:24:35: 6000000 INFO @ Sat, 11 Dec 2021 07:24:36: 10000000 INFO @ Sat, 11 Dec 2021 07:24:44: 14000000 INFO @ Sat, 11 Dec 2021 07:24:47: 11000000 INFO @ Sat, 11 Dec 2021 07:24:48: 7000000 INFO @ Sat, 11 Dec 2021 07:24:55: 15000000 INFO @ Sat, 11 Dec 2021 07:24:58: 12000000 INFO @ Sat, 11 Dec 2021 07:25:01: 8000000 INFO @ Sat, 11 Dec 2021 07:25:06: 16000000 INFO @ Sat, 11 Dec 2021 07:25:09: 13000000 INFO @ Sat, 11 Dec 2021 07:25:14: 9000000 INFO @ Sat, 11 Dec 2021 07:25:17: 17000000 INFO @ Sat, 11 Dec 2021 07:25:20: 14000000 INFO @ Sat, 11 Dec 2021 07:25:26: 10000000 INFO @ Sat, 11 Dec 2021 07:25:29: 18000000 INFO @ Sat, 11 Dec 2021 07:25:32: 15000000 INFO @ Sat, 11 Dec 2021 07:25:38: 11000000 INFO @ Sat, 11 Dec 2021 07:25:40: 19000000 INFO @ Sat, 11 Dec 2021 07:25:43: 16000000 INFO @ Sat, 11 Dec 2021 07:25:51: 12000000 INFO @ Sat, 11 Dec 2021 07:25:51: 20000000 INFO @ Sat, 11 Dec 2021 07:25:55: 17000000 INFO @ Sat, 11 Dec 2021 07:26:03: 21000000 INFO @ Sat, 11 Dec 2021 07:26:03: 13000000 INFO @ Sat, 11 Dec 2021 07:26:06: 18000000 INFO @ Sat, 11 Dec 2021 07:26:14: 22000000 INFO @ Sat, 11 Dec 2021 07:26:16: 14000000 INFO @ Sat, 11 Dec 2021 07:26:18: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:26:25: 23000000 INFO @ Sat, 11 Dec 2021 07:26:28: 15000000 INFO @ Sat, 11 Dec 2021 07:26:29: 20000000 INFO @ Sat, 11 Dec 2021 07:26:37: 24000000 INFO @ Sat, 11 Dec 2021 07:26:40: 16000000 INFO @ Sat, 11 Dec 2021 07:26:40: 21000000 INFO @ Sat, 11 Dec 2021 07:26:48: 25000000 INFO @ Sat, 11 Dec 2021 07:26:51: 22000000 INFO @ Sat, 11 Dec 2021 07:26:52: 17000000 INFO @ Sat, 11 Dec 2021 07:27:00: 26000000 INFO @ Sat, 11 Dec 2021 07:27:03: 23000000 INFO @ Sat, 11 Dec 2021 07:27:05: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:27:11: 27000000 INFO @ Sat, 11 Dec 2021 07:27:14: 24000000 INFO @ Sat, 11 Dec 2021 07:27:18: 19000000 INFO @ Sat, 11 Dec 2021 07:27:23: 28000000 INFO @ Sat, 11 Dec 2021 07:27:26: 25000000 INFO @ Sat, 11 Dec 2021 07:27:30: 20000000 INFO @ Sat, 11 Dec 2021 07:27:34: 29000000 INFO @ Sat, 11 Dec 2021 07:27:37: 26000000 INFO @ Sat, 11 Dec 2021 07:27:42: 21000000 INFO @ Sat, 11 Dec 2021 07:27:45: 30000000 INFO @ Sat, 11 Dec 2021 07:27:49: 27000000 INFO @ Sat, 11 Dec 2021 07:27:55: 22000000 INFO @ Sat, 11 Dec 2021 07:27:57: 31000000 INFO @ Sat, 11 Dec 2021 07:28:00: 28000000 INFO @ Sat, 11 Dec 2021 07:28:07: 23000000 INFO @ Sat, 11 Dec 2021 07:28:08: 32000000 INFO @ Sat, 11 Dec 2021 07:28:11: 29000000 INFO @ Sat, 11 Dec 2021 07:28:19: 33000000 INFO @ Sat, 11 Dec 2021 07:28:20: 24000000 INFO @ Sat, 11 Dec 2021 07:28:23: 30000000 INFO @ Sat, 11 Dec 2021 07:28:31: 34000000 INFO @ Sat, 11 Dec 2021 07:28:32: 25000000 INFO @ Sat, 11 Dec 2021 07:28:34: 31000000 INFO @ Sat, 11 Dec 2021 07:28:42: #1 tag size is determined as 147 bps INFO @ Sat, 11 Dec 2021 07:28:42: #1 tag size = 147 INFO @ Sat, 11 Dec 2021 07:28:42: #1 total tags in treatment: 16670044 INFO @ Sat, 11 Dec 2021 07:28:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:28:42: #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 07:28:42: #1 tags after filtering in treatment: 11112000 INFO @ Sat, 11 Dec 2021 07:28:42: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 07:28:42: #1 finished! INFO @ Sat, 11 Dec 2021 07:28:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:28:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:28:43: #2 number of paired peaks: 1951 INFO @ Sat, 11 Dec 2021 07:28:43: start model_add_line... INFO @ Sat, 11 Dec 2021 07:28:43: start X-correlation... INFO @ Sat, 11 Dec 2021 07:28:43: end of X-cor INFO @ Sat, 11 Dec 2021 07:28:43: #2 finished! INFO @ Sat, 11 Dec 2021 07:28:43: #2 predicted fragment length is 4 bps INFO @ Sat, 11 Dec 2021 07:28:43: #2 alternative fragment length(s) may be 4 bps INFO @ Sat, 11 Dec 2021 07:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.05_model.r WARNING @ Sat, 11 Dec 2021 07:28:43: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:28:43: #2 You may need to consider one of the other alternative d(s): 4 WARNING @ Sat, 11 Dec 2021 07:28:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:28:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:28:44: 26000000 INFO @ Sat, 11 Dec 2021 07:28:45: 32000000 INFO @ Sat, 11 Dec 2021 07:28:55: 33000000 INFO @ Sat, 11 Dec 2021 07:28:56: 27000000 INFO @ Sat, 11 Dec 2021 07:29:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:29:06: 34000000 INFO @ Sat, 11 Dec 2021 07:29:08: 28000000 INFO @ Sat, 11 Dec 2021 07:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.05_summits.bed INFO @ Sat, 11 Dec 2021 07:29:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:29:17: #1 tag size is determined as 147 bps INFO @ Sat, 11 Dec 2021 07:29:17: #1 tag size = 147 INFO @ Sat, 11 Dec 2021 07:29:17: #1 total tags in treatment: 16670044 INFO @ Sat, 11 Dec 2021 07:29:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:17: #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 07:29:17: #1 tags after filtering in treatment: 11112000 INFO @ Sat, 11 Dec 2021 07:29:17: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 07:29:17: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:18: #2 number of paired peaks: 1951 INFO @ Sat, 11 Dec 2021 07:29:18: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:18: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:18: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:18: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:18: #2 predicted fragment length is 4 bps INFO @ Sat, 11 Dec 2021 07:29:18: #2 alternative fragment length(s) may be 4 bps INFO @ Sat, 11 Dec 2021 07:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.10_model.r WARNING @ Sat, 11 Dec 2021 07:29:18: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:29:18: #2 You may need to consider one of the other alternative d(s): 4 WARNING @ Sat, 11 Dec 2021 07:29:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:29:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:29:20: 29000000 INFO @ Sat, 11 Dec 2021 07:29:31: 30000000 INFO @ Sat, 11 Dec 2021 07:29:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:29:42: 31000000 INFO @ Sat, 11 Dec 2021 07:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.10_summits.bed INFO @ Sat, 11 Dec 2021 07:29:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:29:53: 32000000 INFO @ Sat, 11 Dec 2021 07:30:04: 33000000 INFO @ Sat, 11 Dec 2021 07:30:15: 34000000 INFO @ Sat, 11 Dec 2021 07:30:26: #1 tag size is determined as 147 bps INFO @ Sat, 11 Dec 2021 07:30:26: #1 tag size = 147 INFO @ Sat, 11 Dec 2021 07:30:26: #1 total tags in treatment: 16670044 INFO @ Sat, 11 Dec 2021 07:30:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:30:26: #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 07:30:26: #1 tags after filtering in treatment: 11112000 INFO @ Sat, 11 Dec 2021 07:30:26: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 07:30:26: #1 finished! INFO @ Sat, 11 Dec 2021 07:30:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:30:27: #2 number of paired peaks: 1951 INFO @ Sat, 11 Dec 2021 07:30:27: start model_add_line... INFO @ Sat, 11 Dec 2021 07:30:27: start X-correlation... INFO @ Sat, 11 Dec 2021 07:30:27: end of X-cor INFO @ Sat, 11 Dec 2021 07:30:27: #2 finished! INFO @ Sat, 11 Dec 2021 07:30:27: #2 predicted fragment length is 4 bps INFO @ Sat, 11 Dec 2021 07:30:27: #2 alternative fragment length(s) may be 4 bps INFO @ Sat, 11 Dec 2021 07:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.20_model.r WARNING @ Sat, 11 Dec 2021 07:30:27: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:30:27: #2 You may need to consider one of the other alternative d(s): 4 WARNING @ Sat, 11 Dec 2021 07:30:27: #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 07:30:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:30:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10706038/SRX10706038.20_summits.bed INFO @ Sat, 11 Dec 2021 07:31:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling