Job ID = 14171425 SRX = SRX9711632 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18315399 spots for SRR13282247/SRR13282247.sra Written 18315399 spots for SRR13282247/SRR13282247.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172030 ("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: 00:31:50 18315399 reads; of these: 18315399 (100.00%) were paired; of these: 2722256 (14.86%) aligned concordantly 0 times 12882286 (70.34%) aligned concordantly exactly 1 time 2710857 (14.80%) aligned concordantly >1 times ---- 2722256 pairs aligned concordantly 0 times; of these: 1300227 (47.76%) aligned discordantly 1 time ---- 1422029 pairs aligned 0 times concordantly or discordantly; of these: 2844058 mates make up the pairs; of these: 1844242 (64.85%) aligned 0 times 488637 (17.18%) aligned exactly 1 time 511179 (17.97%) aligned >1 times 94.97% overall alignment rate Time searching: 00:31:50 Overall time: 00:31:50 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 16 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] 617522 / 16772122 = 0.0368 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 12:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.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 12:19:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:19:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:19:51: 1000000 INFO @ Sat, 11 Dec 2021 12:19:57: 2000000 INFO @ Sat, 11 Dec 2021 12:20:03: 3000000 INFO @ Sat, 11 Dec 2021 12:20:09: 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 12:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.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 12:20:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:20:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:20:15: 5000000 INFO @ Sat, 11 Dec 2021 12:20:21: 6000000 INFO @ Sat, 11 Dec 2021 12:20:22: 1000000 INFO @ Sat, 11 Dec 2021 12:20:28: 7000000 INFO @ Sat, 11 Dec 2021 12:20:28: 2000000 INFO @ Sat, 11 Dec 2021 12:20:35: 8000000 INFO @ Sat, 11 Dec 2021 12:20:35: 3000000 INFO @ Sat, 11 Dec 2021 12:20:41: 9000000 INFO @ Sat, 11 Dec 2021 12:20:42: 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 12:20:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.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 12:20:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:20:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:20:48: 10000000 INFO @ Sat, 11 Dec 2021 12:20:48: 5000000 INFO @ Sat, 11 Dec 2021 12:20:51: 1000000 INFO @ Sat, 11 Dec 2021 12:20:55: 11000000 INFO @ Sat, 11 Dec 2021 12:20:55: 6000000 INFO @ Sat, 11 Dec 2021 12:20:58: 2000000 INFO @ Sat, 11 Dec 2021 12:21:02: 7000000 INFO @ Sat, 11 Dec 2021 12:21:02: 12000000 INFO @ Sat, 11 Dec 2021 12:21:05: 3000000 INFO @ Sat, 11 Dec 2021 12:21:09: 8000000 INFO @ Sat, 11 Dec 2021 12:21:09: 13000000 INFO @ Sat, 11 Dec 2021 12:21:12: 4000000 INFO @ Sat, 11 Dec 2021 12:21:15: 9000000 INFO @ Sat, 11 Dec 2021 12:21:16: 14000000 INFO @ Sat, 11 Dec 2021 12:21:19: 5000000 INFO @ Sat, 11 Dec 2021 12:21:22: 10000000 INFO @ Sat, 11 Dec 2021 12:21:23: 15000000 INFO @ Sat, 11 Dec 2021 12:21:26: 6000000 INFO @ Sat, 11 Dec 2021 12:21:29: 11000000 INFO @ Sat, 11 Dec 2021 12:21:29: 16000000 INFO @ Sat, 11 Dec 2021 12:21:33: 7000000 INFO @ Sat, 11 Dec 2021 12:21:36: 12000000 INFO @ Sat, 11 Dec 2021 12:21:36: 17000000 INFO @ Sat, 11 Dec 2021 12:21:40: 8000000 INFO @ Sat, 11 Dec 2021 12:21:42: 13000000 INFO @ Sat, 11 Dec 2021 12:21:43: 18000000 INFO @ Sat, 11 Dec 2021 12:21:47: 9000000 INFO @ Sat, 11 Dec 2021 12:21:49: 14000000 INFO @ Sat, 11 Dec 2021 12:21:50: 19000000 INFO @ Sat, 11 Dec 2021 12:21:54: 10000000 INFO @ Sat, 11 Dec 2021 12:21:56: 15000000 INFO @ Sat, 11 Dec 2021 12:21:57: 20000000 INFO @ Sat, 11 Dec 2021 12:22:00: 11000000 INFO @ Sat, 11 Dec 2021 12:22:03: 16000000 INFO @ Sat, 11 Dec 2021 12:22:04: 21000000 INFO @ Sat, 11 Dec 2021 12:22:07: 12000000 INFO @ Sat, 11 Dec 2021 12:22:09: 17000000 INFO @ Sat, 11 Dec 2021 12:22:11: 22000000 INFO @ Sat, 11 Dec 2021 12:22:14: 13000000 INFO @ Sat, 11 Dec 2021 12:22:16: 18000000 INFO @ Sat, 11 Dec 2021 12:22:18: 23000000 INFO @ Sat, 11 Dec 2021 12:22:21: 14000000 INFO @ Sat, 11 Dec 2021 12:22:22: 19000000 INFO @ Sat, 11 Dec 2021 12:22:24: 24000000 INFO @ Sat, 11 Dec 2021 12:22:28: 15000000 INFO @ Sat, 11 Dec 2021 12:22:29: 20000000 INFO @ Sat, 11 Dec 2021 12:22:31: 25000000 INFO @ Sat, 11 Dec 2021 12:22:35: 16000000 INFO @ Sat, 11 Dec 2021 12:22:36: 21000000 INFO @ Sat, 11 Dec 2021 12:22:38: 26000000 INFO @ Sat, 11 Dec 2021 12:22:42: 17000000 INFO @ Sat, 11 Dec 2021 12:22:42: 22000000 INFO @ Sat, 11 Dec 2021 12:22:45: 27000000 INFO @ Sat, 11 Dec 2021 12:22:49: 18000000 INFO @ Sat, 11 Dec 2021 12:22:49: 23000000 INFO @ Sat, 11 Dec 2021 12:22:52: 28000000 INFO @ Sat, 11 Dec 2021 12:22:56: 19000000 INFO @ Sat, 11 Dec 2021 12:22:56: 24000000 INFO @ Sat, 11 Dec 2021 12:22:59: 29000000 INFO @ Sat, 11 Dec 2021 12:23:03: 20000000 INFO @ Sat, 11 Dec 2021 12:23:03: 25000000 INFO @ Sat, 11 Dec 2021 12:23:06: 30000000 INFO @ Sat, 11 Dec 2021 12:23:10: 21000000 INFO @ Sat, 11 Dec 2021 12:23:10: 26000000 INFO @ Sat, 11 Dec 2021 12:23:14: 31000000 INFO @ Sat, 11 Dec 2021 12:23:17: 27000000 INFO @ Sat, 11 Dec 2021 12:23:17: 22000000 INFO @ Sat, 11 Dec 2021 12:23:21: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:23:24: 28000000 INFO @ Sat, 11 Dec 2021 12:23:24: 23000000 INFO @ Sat, 11 Dec 2021 12:23:28: 33000000 INFO @ Sat, 11 Dec 2021 12:23:30: 29000000 INFO @ Sat, 11 Dec 2021 12:23:31: 24000000 INFO @ Sat, 11 Dec 2021 12:23:31: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:23:31: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:23:31: #1 total tags in treatment: 15013107 INFO @ Sat, 11 Dec 2021 12:23:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:23:31: #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 12:23:32: #1 tags after filtering in treatment: 14089520 INFO @ Sat, 11 Dec 2021 12:23:32: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:23:32: #1 finished! INFO @ Sat, 11 Dec 2021 12:23:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:23:32: #2 number of paired peaks: 104 WARNING @ Sat, 11 Dec 2021 12:23:32: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sat, 11 Dec 2021 12:23:32: start model_add_line... INFO @ Sat, 11 Dec 2021 12:23:33: start X-correlation... INFO @ Sat, 11 Dec 2021 12:23:33: end of X-cor INFO @ Sat, 11 Dec 2021 12:23:33: #2 finished! INFO @ Sat, 11 Dec 2021 12:23:33: #2 predicted fragment length is 157 bps INFO @ Sat, 11 Dec 2021 12:23:33: #2 alternative fragment length(s) may be 3,134,157 bps INFO @ Sat, 11 Dec 2021 12:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.05_model.r WARNING @ Sat, 11 Dec 2021 12:23:33: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:23:33: #2 You may need to consider one of the other alternative d(s): 3,134,157 WARNING @ Sat, 11 Dec 2021 12:23:33: #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 12:23:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:23:37: 30000000 INFO @ Sat, 11 Dec 2021 12:23:38: 25000000 INFO @ Sat, 11 Dec 2021 12:23:44: 31000000 INFO @ Sat, 11 Dec 2021 12:23:44: 26000000 INFO @ Sat, 11 Dec 2021 12:23:50: 32000000 INFO @ Sat, 11 Dec 2021 12:23:51: 27000000 INFO @ Sat, 11 Dec 2021 12:23:57: 33000000 INFO @ Sat, 11 Dec 2021 12:23:58: 28000000 INFO @ Sat, 11 Dec 2021 12:23:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:24:01: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:24:01: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:24:01: #1 total tags in treatment: 15013107 INFO @ Sat, 11 Dec 2021 12:24:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:24:01: #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 12:24:01: #1 tags after filtering in treatment: 14089520 INFO @ Sat, 11 Dec 2021 12:24:01: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:24:01: #1 finished! INFO @ Sat, 11 Dec 2021 12:24:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:24:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:24:02: #2 number of paired peaks: 104 WARNING @ Sat, 11 Dec 2021 12:24:02: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sat, 11 Dec 2021 12:24:02: start model_add_line... INFO @ Sat, 11 Dec 2021 12:24:02: start X-correlation... INFO @ Sat, 11 Dec 2021 12:24:02: end of X-cor INFO @ Sat, 11 Dec 2021 12:24:02: #2 finished! INFO @ Sat, 11 Dec 2021 12:24:02: #2 predicted fragment length is 157 bps INFO @ Sat, 11 Dec 2021 12:24:02: #2 alternative fragment length(s) may be 3,134,157 bps INFO @ Sat, 11 Dec 2021 12:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.10_model.r WARNING @ Sat, 11 Dec 2021 12:24:02: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:24:02: #2 You may need to consider one of the other alternative d(s): 3,134,157 WARNING @ Sat, 11 Dec 2021 12:24:02: #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 12:24:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:24:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:24:04: 29000000 INFO @ Sat, 11 Dec 2021 12:24:10: 30000000 INFO @ Sat, 11 Dec 2021 12:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:24:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.05_summits.bed INFO @ Sat, 11 Dec 2021 12:24:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:24:16: 31000000 INFO @ Sat, 11 Dec 2021 12:24:21: 32000000 INFO @ Sat, 11 Dec 2021 12:24:27: 33000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:24:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:24:30: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:24:30: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:24:30: #1 total tags in treatment: 15013107 INFO @ Sat, 11 Dec 2021 12:24:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:24:30: #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 12:24:31: #1 tags after filtering in treatment: 14089520 INFO @ Sat, 11 Dec 2021 12:24:31: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:24:31: #1 finished! INFO @ Sat, 11 Dec 2021 12:24:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:24:32: #2 number of paired peaks: 104 WARNING @ Sat, 11 Dec 2021 12:24:32: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sat, 11 Dec 2021 12:24:32: start model_add_line... INFO @ Sat, 11 Dec 2021 12:24:32: start X-correlation... INFO @ Sat, 11 Dec 2021 12:24:32: end of X-cor INFO @ Sat, 11 Dec 2021 12:24:32: #2 finished! INFO @ Sat, 11 Dec 2021 12:24:32: #2 predicted fragment length is 157 bps INFO @ Sat, 11 Dec 2021 12:24:32: #2 alternative fragment length(s) may be 3,134,157 bps INFO @ Sat, 11 Dec 2021 12:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.20_model.r WARNING @ Sat, 11 Dec 2021 12:24:32: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:24:32: #2 You may need to consider one of the other alternative d(s): 3,134,157 WARNING @ Sat, 11 Dec 2021 12:24:32: #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 12:24:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:24:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.10_summits.bed INFO @ Sat, 11 Dec 2021 12:24:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:24:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:25:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:25:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:25:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711632/SRX9711632.20_summits.bed INFO @ Sat, 11 Dec 2021 12:25:10: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (84 records, 4 fields): 2 millis CompletedMACS2peakCalling