Job ID = 12265558 SRX = SRX7277023 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28415384 spots for SRR10597288/SRR10597288.sra Written 28415384 spots for SRR10597288/SRR10597288.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265824 ("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: 00:38:13 28415384 reads; of these: 28415384 (100.00%) were paired; of these: 11040268 (38.85%) aligned concordantly 0 times 11344441 (39.92%) aligned concordantly exactly 1 time 6030675 (21.22%) aligned concordantly >1 times ---- 11040268 pairs aligned concordantly 0 times; of these: 2909701 (26.36%) aligned discordantly 1 time ---- 8130567 pairs aligned 0 times concordantly or discordantly; of these: 16261134 mates make up the pairs; of these: 12849653 (79.02%) aligned 0 times 775350 (4.77%) aligned exactly 1 time 2636131 (16.21%) aligned >1 times 77.39% overall alignment rate Time searching: 00:38:13 Overall time: 00:38:13 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 20 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] 4449539 / 20124302 = 0.2211 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:30:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.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, 03 Apr 2021 08:30:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:30:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:30:37: 1000000 INFO @ Sat, 03 Apr 2021 08:30:44: 2000000 INFO @ Sat, 03 Apr 2021 08:30:50: 3000000 INFO @ Sat, 03 Apr 2021 08:30:57: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:31:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.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, 03 Apr 2021 08:31:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:31:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:31:04: 5000000 INFO @ Sat, 03 Apr 2021 08:31:08: 1000000 INFO @ Sat, 03 Apr 2021 08:31:11: 6000000 INFO @ Sat, 03 Apr 2021 08:31:16: 2000000 INFO @ Sat, 03 Apr 2021 08:31:18: 7000000 INFO @ Sat, 03 Apr 2021 08:31:23: 3000000 INFO @ Sat, 03 Apr 2021 08:31:26: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:31:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.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, 03 Apr 2021 08:31:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:31:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:31:31: 4000000 INFO @ Sat, 03 Apr 2021 08:31:33: 9000000 INFO @ Sat, 03 Apr 2021 08:31:38: 1000000 INFO @ Sat, 03 Apr 2021 08:31:39: 5000000 INFO @ Sat, 03 Apr 2021 08:31:40: 10000000 INFO @ Sat, 03 Apr 2021 08:31:46: 2000000 INFO @ Sat, 03 Apr 2021 08:31:47: 6000000 INFO @ Sat, 03 Apr 2021 08:31:48: 11000000 INFO @ Sat, 03 Apr 2021 08:31:53: 3000000 INFO @ Sat, 03 Apr 2021 08:31:54: 7000000 INFO @ Sat, 03 Apr 2021 08:31:56: 12000000 INFO @ Sat, 03 Apr 2021 08:32:01: 4000000 INFO @ Sat, 03 Apr 2021 08:32:02: 8000000 INFO @ Sat, 03 Apr 2021 08:32:03: 13000000 INFO @ Sat, 03 Apr 2021 08:32:08: 5000000 INFO @ Sat, 03 Apr 2021 08:32:10: 9000000 INFO @ Sat, 03 Apr 2021 08:32:11: 14000000 INFO @ Sat, 03 Apr 2021 08:32:16: 6000000 INFO @ Sat, 03 Apr 2021 08:32:18: 10000000 INFO @ Sat, 03 Apr 2021 08:32:18: 15000000 INFO @ Sat, 03 Apr 2021 08:32:24: 7000000 INFO @ Sat, 03 Apr 2021 08:32:25: 11000000 INFO @ Sat, 03 Apr 2021 08:32:26: 16000000 INFO @ Sat, 03 Apr 2021 08:32:31: 8000000 INFO @ Sat, 03 Apr 2021 08:32:33: 12000000 INFO @ Sat, 03 Apr 2021 08:32:34: 17000000 INFO @ Sat, 03 Apr 2021 08:32:39: 9000000 INFO @ Sat, 03 Apr 2021 08:32:41: 13000000 INFO @ Sat, 03 Apr 2021 08:32:41: 18000000 INFO @ Sat, 03 Apr 2021 08:32:46: 10000000 INFO @ Sat, 03 Apr 2021 08:32:48: 14000000 INFO @ Sat, 03 Apr 2021 08:32:49: 19000000 INFO @ Sat, 03 Apr 2021 08:32:54: 11000000 INFO @ Sat, 03 Apr 2021 08:32:56: 20000000 INFO @ Sat, 03 Apr 2021 08:32:56: 15000000 INFO @ Sat, 03 Apr 2021 08:33:01: 12000000 INFO @ Sat, 03 Apr 2021 08:33:03: 21000000 INFO @ Sat, 03 Apr 2021 08:33:04: 16000000 INFO @ Sat, 03 Apr 2021 08:33:09: 13000000 INFO @ Sat, 03 Apr 2021 08:33:11: 22000000 INFO @ Sat, 03 Apr 2021 08:33:11: 17000000 INFO @ Sat, 03 Apr 2021 08:33:17: 14000000 INFO @ Sat, 03 Apr 2021 08:33:18: 23000000 INFO @ Sat, 03 Apr 2021 08:33:19: 18000000 INFO @ Sat, 03 Apr 2021 08:33:24: 15000000 INFO @ Sat, 03 Apr 2021 08:33:25: 24000000 INFO @ Sat, 03 Apr 2021 08:33:26: 19000000 INFO @ Sat, 03 Apr 2021 08:33:32: 16000000 INFO @ Sat, 03 Apr 2021 08:33:33: 25000000 INFO @ Sat, 03 Apr 2021 08:33:34: 20000000 INFO @ Sat, 03 Apr 2021 08:33:39: 17000000 INFO @ Sat, 03 Apr 2021 08:33:40: 26000000 INFO @ Sat, 03 Apr 2021 08:33:41: 21000000 INFO @ Sat, 03 Apr 2021 08:33:47: 18000000 INFO @ Sat, 03 Apr 2021 08:33:47: 27000000 INFO @ Sat, 03 Apr 2021 08:33:49: 22000000 INFO @ Sat, 03 Apr 2021 08:33:54: 28000000 INFO @ Sat, 03 Apr 2021 08:33:54: 19000000 INFO @ Sat, 03 Apr 2021 08:33:56: 23000000 INFO @ Sat, 03 Apr 2021 08:34:02: 29000000 INFO @ Sat, 03 Apr 2021 08:34:02: 20000000 INFO @ Sat, 03 Apr 2021 08:34:03: 24000000 INFO @ Sat, 03 Apr 2021 08:34:09: 30000000 INFO @ Sat, 03 Apr 2021 08:34:10: 21000000 INFO @ Sat, 03 Apr 2021 08:34:11: 25000000 INFO @ Sat, 03 Apr 2021 08:34:17: 31000000 INFO @ Sat, 03 Apr 2021 08:34:17: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:34:18: 26000000 INFO @ Sat, 03 Apr 2021 08:34:24: 32000000 INFO @ Sat, 03 Apr 2021 08:34:25: 23000000 INFO @ Sat, 03 Apr 2021 08:34:25: 27000000 INFO @ Sat, 03 Apr 2021 08:34:31: 33000000 INFO @ Sat, 03 Apr 2021 08:34:32: 24000000 INFO @ Sat, 03 Apr 2021 08:34:33: 28000000 INFO @ Sat, 03 Apr 2021 08:34:38: 34000000 INFO @ Sat, 03 Apr 2021 08:34:40: 25000000 INFO @ Sat, 03 Apr 2021 08:34:40: 29000000 INFO @ Sat, 03 Apr 2021 08:34:46: 35000000 INFO @ Sat, 03 Apr 2021 08:34:46: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:34:46: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:34:46: #1 total tags in treatment: 13141222 INFO @ Sat, 03 Apr 2021 08:34:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:34:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:34:47: #1 tags after filtering in treatment: 10416467 INFO @ Sat, 03 Apr 2021 08:34:47: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:34:47: #1 finished! INFO @ Sat, 03 Apr 2021 08:34:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:34:47: 26000000 INFO @ Sat, 03 Apr 2021 08:34:47: #2 number of paired peaks: 285 WARNING @ Sat, 03 Apr 2021 08:34:47: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sat, 03 Apr 2021 08:34:47: start model_add_line... INFO @ Sat, 03 Apr 2021 08:34:48: start X-correlation... INFO @ Sat, 03 Apr 2021 08:34:48: end of X-cor INFO @ Sat, 03 Apr 2021 08:34:48: #2 finished! INFO @ Sat, 03 Apr 2021 08:34:48: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 08:34:48: #2 alternative fragment length(s) may be 4,76,96 bps INFO @ Sat, 03 Apr 2021 08:34:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.05_model.r WARNING @ Sat, 03 Apr 2021 08:34:48: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:34:48: #2 You may need to consider one of the other alternative d(s): 4,76,96 WARNING @ Sat, 03 Apr 2021 08:34:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:34:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:34:48: 30000000 INFO @ Sat, 03 Apr 2021 08:34:55: 27000000 INFO @ Sat, 03 Apr 2021 08:34:55: 31000000 INFO @ Sat, 03 Apr 2021 08:35:02: 28000000 INFO @ Sat, 03 Apr 2021 08:35:02: 32000000 INFO @ Sat, 03 Apr 2021 08:35:10: 33000000 INFO @ Sat, 03 Apr 2021 08:35:10: 29000000 INFO @ Sat, 03 Apr 2021 08:35:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:35:17: 34000000 INFO @ Sat, 03 Apr 2021 08:35:17: 30000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.05_summits.bed INFO @ Sat, 03 Apr 2021 08:35:24: Done! INFO @ Sat, 03 Apr 2021 08:35:24: 35000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5275 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:35:24: 31000000 INFO @ Sat, 03 Apr 2021 08:35:25: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:35:25: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:35:25: #1 total tags in treatment: 13141222 INFO @ Sat, 03 Apr 2021 08:35:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:35:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:35:25: #1 tags after filtering in treatment: 10416467 INFO @ Sat, 03 Apr 2021 08:35:25: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:35:25: #1 finished! INFO @ Sat, 03 Apr 2021 08:35:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:35:26: #2 number of paired peaks: 285 WARNING @ Sat, 03 Apr 2021 08:35:26: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sat, 03 Apr 2021 08:35:26: start model_add_line... INFO @ Sat, 03 Apr 2021 08:35:26: start X-correlation... INFO @ Sat, 03 Apr 2021 08:35:26: end of X-cor INFO @ Sat, 03 Apr 2021 08:35:26: #2 finished! INFO @ Sat, 03 Apr 2021 08:35:26: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 08:35:26: #2 alternative fragment length(s) may be 4,76,96 bps INFO @ Sat, 03 Apr 2021 08:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.10_model.r WARNING @ Sat, 03 Apr 2021 08:35:26: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:35:26: #2 You may need to consider one of the other alternative d(s): 4,76,96 WARNING @ Sat, 03 Apr 2021 08:35:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:35:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:35:31: 32000000 INFO @ Sat, 03 Apr 2021 08:35:38: 33000000 INFO @ Sat, 03 Apr 2021 08:35:45: 34000000 INFO @ Sat, 03 Apr 2021 08:35:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:35:51: 35000000 INFO @ Sat, 03 Apr 2021 08:35:52: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:35:52: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:35:52: #1 total tags in treatment: 13141222 INFO @ Sat, 03 Apr 2021 08:35:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:35:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:35:52: #1 tags after filtering in treatment: 10416467 INFO @ Sat, 03 Apr 2021 08:35:52: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:35:52: #1 finished! INFO @ Sat, 03 Apr 2021 08:35:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:35:53: #2 number of paired peaks: 285 WARNING @ Sat, 03 Apr 2021 08:35:53: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sat, 03 Apr 2021 08:35:53: start model_add_line... INFO @ Sat, 03 Apr 2021 08:35:53: start X-correlation... INFO @ Sat, 03 Apr 2021 08:35:53: end of X-cor INFO @ Sat, 03 Apr 2021 08:35:53: #2 finished! INFO @ Sat, 03 Apr 2021 08:35:53: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 08:35:53: #2 alternative fragment length(s) may be 4,76,96 bps INFO @ Sat, 03 Apr 2021 08:35:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.20_model.r WARNING @ Sat, 03 Apr 2021 08:35:53: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:35:53: #2 You may need to consider one of the other alternative d(s): 4,76,96 WARNING @ Sat, 03 Apr 2021 08:35:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:35:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:36:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:36:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:36:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.10_summits.bed INFO @ Sat, 03 Apr 2021 08:36:03: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1046 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:36:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277023/SRX7277023.20_summits.bed INFO @ Sat, 03 Apr 2021 08:36:30: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (101 records, 4 fields): 1 millis CompletedMACS2peakCalling