Job ID = 14170605 SRX = SRX8497059 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19309273 spots for SRR11952658/SRR11952658.sra Written 19309273 spots for SRR11952658/SRR11952658.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171164 ("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: 00:50:51 19309273 reads; of these: 19309273 (100.00%) were paired; of these: 1808752 (9.37%) aligned concordantly 0 times 11990991 (62.10%) aligned concordantly exactly 1 time 5509530 (28.53%) aligned concordantly >1 times ---- 1808752 pairs aligned concordantly 0 times; of these: 286308 (15.83%) aligned discordantly 1 time ---- 1522444 pairs aligned 0 times concordantly or discordantly; of these: 3044888 mates make up the pairs; of these: 2144754 (70.44%) aligned 0 times 465251 (15.28%) aligned exactly 1 time 434883 (14.28%) aligned >1 times 94.45% overall alignment rate Time searching: 00:50:51 Overall time: 00:50:51 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] 2183679 / 17748873 = 0.1230 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 08:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.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 08:30:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:30:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:30:08: 1000000 INFO @ Sat, 11 Dec 2021 08:30:13: 2000000 INFO @ Sat, 11 Dec 2021 08:30:19: 3000000 INFO @ Sat, 11 Dec 2021 08:30:24: 4000000 INFO @ Sat, 11 Dec 2021 08:30:30: 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 08:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.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 08:30:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:30:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:30:36: 6000000 INFO @ Sat, 11 Dec 2021 08:30:38: 1000000 INFO @ Sat, 11 Dec 2021 08:30:42: 7000000 INFO @ Sat, 11 Dec 2021 08:30:46: 2000000 INFO @ Sat, 11 Dec 2021 08:30:48: 8000000 INFO @ Sat, 11 Dec 2021 08:30:53: 3000000 INFO @ Sat, 11 Dec 2021 08:30:54: 9000000 INFO @ Sat, 11 Dec 2021 08:31:00: 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 08:31:01: 10000000 INFO @ Sat, 11 Dec 2021 08:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.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 08:31:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:31:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:31:07: 5000000 INFO @ Sat, 11 Dec 2021 08:31:07: 11000000 INFO @ Sat, 11 Dec 2021 08:31:08: 1000000 INFO @ Sat, 11 Dec 2021 08:31:13: 12000000 INFO @ Sat, 11 Dec 2021 08:31:14: 6000000 INFO @ Sat, 11 Dec 2021 08:31:15: 2000000 INFO @ Sat, 11 Dec 2021 08:31:20: 13000000 INFO @ Sat, 11 Dec 2021 08:31:21: 7000000 INFO @ Sat, 11 Dec 2021 08:31:21: 3000000 INFO @ Sat, 11 Dec 2021 08:31:26: 14000000 INFO @ Sat, 11 Dec 2021 08:31:27: 4000000 INFO @ Sat, 11 Dec 2021 08:31:28: 8000000 INFO @ Sat, 11 Dec 2021 08:31:32: 15000000 INFO @ Sat, 11 Dec 2021 08:31:34: 5000000 INFO @ Sat, 11 Dec 2021 08:31:35: 9000000 INFO @ Sat, 11 Dec 2021 08:31:39: 16000000 INFO @ Sat, 11 Dec 2021 08:31:40: 6000000 INFO @ Sat, 11 Dec 2021 08:31:42: 10000000 INFO @ Sat, 11 Dec 2021 08:31:45: 17000000 INFO @ Sat, 11 Dec 2021 08:31:47: 7000000 INFO @ Sat, 11 Dec 2021 08:31:49: 11000000 INFO @ Sat, 11 Dec 2021 08:31:51: 18000000 INFO @ Sat, 11 Dec 2021 08:31:53: 8000000 INFO @ Sat, 11 Dec 2021 08:31:56: 12000000 INFO @ Sat, 11 Dec 2021 08:31:58: 19000000 INFO @ Sat, 11 Dec 2021 08:31:59: 9000000 INFO @ Sat, 11 Dec 2021 08:32:03: 13000000 INFO @ Sat, 11 Dec 2021 08:32:04: 20000000 INFO @ Sat, 11 Dec 2021 08:32:06: 10000000 INFO @ Sat, 11 Dec 2021 08:32:10: 21000000 INFO @ Sat, 11 Dec 2021 08:32:10: 14000000 INFO @ Sat, 11 Dec 2021 08:32:12: 11000000 INFO @ Sat, 11 Dec 2021 08:32:16: 22000000 INFO @ Sat, 11 Dec 2021 08:32:17: 15000000 INFO @ Sat, 11 Dec 2021 08:32:18: 12000000 INFO @ Sat, 11 Dec 2021 08:32:23: 23000000 INFO @ Sat, 11 Dec 2021 08:32:24: 16000000 INFO @ Sat, 11 Dec 2021 08:32:24: 13000000 INFO @ Sat, 11 Dec 2021 08:32:29: 24000000 INFO @ Sat, 11 Dec 2021 08:32:31: 14000000 INFO @ Sat, 11 Dec 2021 08:32:31: 17000000 INFO @ Sat, 11 Dec 2021 08:32:35: 25000000 INFO @ Sat, 11 Dec 2021 08:32:37: 15000000 INFO @ Sat, 11 Dec 2021 08:32:38: 18000000 INFO @ Sat, 11 Dec 2021 08:32:42: 26000000 INFO @ Sat, 11 Dec 2021 08:32:43: 16000000 INFO @ Sat, 11 Dec 2021 08:32:45: 19000000 INFO @ Sat, 11 Dec 2021 08:32:48: 27000000 INFO @ Sat, 11 Dec 2021 08:32:50: 17000000 INFO @ Sat, 11 Dec 2021 08:32:52: 20000000 INFO @ Sat, 11 Dec 2021 08:32:55: 28000000 INFO @ Sat, 11 Dec 2021 08:32:56: 18000000 INFO @ Sat, 11 Dec 2021 08:32:59: 21000000 INFO @ Sat, 11 Dec 2021 08:33:01: 29000000 INFO @ Sat, 11 Dec 2021 08:33:02: 19000000 INFO @ Sat, 11 Dec 2021 08:33:06: 22000000 INFO @ Sat, 11 Dec 2021 08:33:07: 30000000 INFO @ Sat, 11 Dec 2021 08:33:09: 20000000 INFO @ Sat, 11 Dec 2021 08:33:14: 23000000 INFO @ Sat, 11 Dec 2021 08:33:14: 31000000 INFO @ Sat, 11 Dec 2021 08:33:15: 21000000 INFO @ Sat, 11 Dec 2021 08:33:20: 32000000 INFO @ Sat, 11 Dec 2021 08:33:21: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:33:21: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:33:21: #1 total tags in treatment: 15338811 INFO @ Sat, 11 Dec 2021 08:33:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:33:21: #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 08:33:21: #1 tags after filtering in treatment: 14316167 INFO @ Sat, 11 Dec 2021 08:33:21: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 08:33:21: #1 finished! INFO @ Sat, 11 Dec 2021 08:33:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:33:21: 24000000 INFO @ Sat, 11 Dec 2021 08:33:21: 22000000 INFO @ Sat, 11 Dec 2021 08:33:22: #2 number of paired peaks: 224 WARNING @ Sat, 11 Dec 2021 08:33:22: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Sat, 11 Dec 2021 08:33:22: start model_add_line... INFO @ Sat, 11 Dec 2021 08:33:22: start X-correlation... INFO @ Sat, 11 Dec 2021 08:33:22: end of X-cor INFO @ Sat, 11 Dec 2021 08:33:22: #2 finished! INFO @ Sat, 11 Dec 2021 08:33:22: #2 predicted fragment length is 191 bps INFO @ Sat, 11 Dec 2021 08:33:22: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 11 Dec 2021 08:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.05_model.r WARNING @ Sat, 11 Dec 2021 08:33:22: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:33:22: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 11 Dec 2021 08:33:22: #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 08:33:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:33:28: 23000000 INFO @ Sat, 11 Dec 2021 08:33:28: 25000000 INFO @ Sat, 11 Dec 2021 08:33:34: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:33:36: 26000000 INFO @ Sat, 11 Dec 2021 08:33:40: 25000000 INFO @ Sat, 11 Dec 2021 08:33:43: 27000000 INFO @ Sat, 11 Dec 2021 08:33:47: 26000000 INFO @ Sat, 11 Dec 2021 08:33:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:33:50: 28000000 INFO @ Sat, 11 Dec 2021 08:33:53: 27000000 INFO @ Sat, 11 Dec 2021 08:33:57: 29000000 INFO @ Sat, 11 Dec 2021 08:33:59: 28000000 INFO @ Sat, 11 Dec 2021 08:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:34:04: 30000000 INFO @ Sat, 11 Dec 2021 08:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.05_summits.bed INFO @ Sat, 11 Dec 2021 08:34:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4016 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:34:06: 29000000 INFO @ Sat, 11 Dec 2021 08:34:11: 31000000 INFO @ Sat, 11 Dec 2021 08:34:12: 30000000 INFO @ Sat, 11 Dec 2021 08:34:18: 31000000 INFO @ Sat, 11 Dec 2021 08:34:19: 32000000 INFO @ Sat, 11 Dec 2021 08:34:19: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:34:19: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:34:19: #1 total tags in treatment: 15338811 INFO @ Sat, 11 Dec 2021 08:34:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:34:19: #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 08:34:20: #1 tags after filtering in treatment: 14316167 INFO @ Sat, 11 Dec 2021 08:34:20: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 08:34:20: #1 finished! INFO @ Sat, 11 Dec 2021 08:34:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:34:21: #2 number of paired peaks: 224 WARNING @ Sat, 11 Dec 2021 08:34:21: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Sat, 11 Dec 2021 08:34:21: start model_add_line... INFO @ Sat, 11 Dec 2021 08:34:21: start X-correlation... INFO @ Sat, 11 Dec 2021 08:34:21: end of X-cor INFO @ Sat, 11 Dec 2021 08:34:21: #2 finished! INFO @ Sat, 11 Dec 2021 08:34:21: #2 predicted fragment length is 191 bps INFO @ Sat, 11 Dec 2021 08:34:21: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 11 Dec 2021 08:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.10_model.r WARNING @ Sat, 11 Dec 2021 08:34:21: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:34:21: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 11 Dec 2021 08:34:21: #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 08:34:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:34:24: 32000000 INFO @ Sat, 11 Dec 2021 08:34:25: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:34:25: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:34:25: #1 total tags in treatment: 15338811 INFO @ Sat, 11 Dec 2021 08:34:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:34:25: #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 08:34:25: #1 tags after filtering in treatment: 14316167 INFO @ Sat, 11 Dec 2021 08:34:25: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 08:34:25: #1 finished! INFO @ Sat, 11 Dec 2021 08:34:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:34:26: #2 number of paired peaks: 224 WARNING @ Sat, 11 Dec 2021 08:34:26: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Sat, 11 Dec 2021 08:34:26: start model_add_line... INFO @ Sat, 11 Dec 2021 08:34:26: start X-correlation... INFO @ Sat, 11 Dec 2021 08:34:26: end of X-cor INFO @ Sat, 11 Dec 2021 08:34:26: #2 finished! INFO @ Sat, 11 Dec 2021 08:34:26: #2 predicted fragment length is 191 bps INFO @ Sat, 11 Dec 2021 08:34:26: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 11 Dec 2021 08:34:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.20_model.r WARNING @ Sat, 11 Dec 2021 08:34:26: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:34:26: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 11 Dec 2021 08:34:26: #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 08:34:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:34:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:34:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:34:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.10_summits.bed INFO @ Sat, 11 Dec 2021 08:35:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2043 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497059/SRX8497059.20_summits.bed INFO @ Sat, 11 Dec 2021 08:35:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 2 millis CompletedMACS2peakCalling