Job ID = 14167074 SRX = SRX10412056 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16738152 spots for SRR14035720/SRR14035720.sra Written 16738152 spots for SRR14035720/SRR14035720.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167677 ("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: 01:11:33 16738152 reads; of these: 16738152 (100.00%) were paired; of these: 1843222 (11.01%) aligned concordantly 0 times 10184774 (60.85%) aligned concordantly exactly 1 time 4710156 (28.14%) aligned concordantly >1 times ---- 1843222 pairs aligned concordantly 0 times; of these: 283608 (15.39%) aligned discordantly 1 time ---- 1559614 pairs aligned 0 times concordantly or discordantly; of these: 3119228 mates make up the pairs; of these: 2333472 (74.81%) aligned 0 times 279651 (8.97%) aligned exactly 1 time 506105 (16.23%) aligned >1 times 93.03% overall alignment rate Time searching: 01:11:34 Overall time: 01:11:34 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 24 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] 3396792 / 15115209 = 0.2247 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 @ Fri, 10 Dec 2021 10:59:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.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 @ Fri, 10 Dec 2021 10:59:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:59:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:59:48: 1000000 INFO @ Fri, 10 Dec 2021 10:59:57: 2000000 INFO @ Fri, 10 Dec 2021 11:00:06: 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 @ Fri, 10 Dec 2021 11:00:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.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 @ Fri, 10 Dec 2021 11:00:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:16: 4000000 INFO @ Fri, 10 Dec 2021 11:00:19: 1000000 INFO @ Fri, 10 Dec 2021 11:00:26: 5000000 INFO @ Fri, 10 Dec 2021 11:00:28: 2000000 INFO @ Fri, 10 Dec 2021 11:00:36: 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 @ Fri, 10 Dec 2021 11:00:38: 3000000 INFO @ Fri, 10 Dec 2021 11:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.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 @ Fri, 10 Dec 2021 11:00:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:45: 7000000 INFO @ Fri, 10 Dec 2021 11:00:47: 4000000 INFO @ Fri, 10 Dec 2021 11:00:48: 1000000 INFO @ Fri, 10 Dec 2021 11:00:55: 8000000 INFO @ Fri, 10 Dec 2021 11:00:57: 2000000 INFO @ Fri, 10 Dec 2021 11:00:57: 5000000 INFO @ Fri, 10 Dec 2021 11:01:05: 9000000 INFO @ Fri, 10 Dec 2021 11:01:06: 3000000 INFO @ Fri, 10 Dec 2021 11:01:07: 6000000 INFO @ Fri, 10 Dec 2021 11:01:14: 4000000 INFO @ Fri, 10 Dec 2021 11:01:15: 10000000 INFO @ Fri, 10 Dec 2021 11:01:17: 7000000 INFO @ Fri, 10 Dec 2021 11:01:23: 5000000 INFO @ Fri, 10 Dec 2021 11:01:25: 11000000 INFO @ Fri, 10 Dec 2021 11:01:26: 8000000 INFO @ Fri, 10 Dec 2021 11:01:31: 6000000 INFO @ Fri, 10 Dec 2021 11:01:34: 12000000 INFO @ Fri, 10 Dec 2021 11:01:36: 9000000 INFO @ Fri, 10 Dec 2021 11:01:40: 7000000 INFO @ Fri, 10 Dec 2021 11:01:44: 13000000 INFO @ Fri, 10 Dec 2021 11:01:46: 10000000 INFO @ Fri, 10 Dec 2021 11:01:48: 8000000 INFO @ Fri, 10 Dec 2021 11:01:54: 14000000 INFO @ Fri, 10 Dec 2021 11:01:55: 11000000 INFO @ Fri, 10 Dec 2021 11:01:57: 9000000 INFO @ Fri, 10 Dec 2021 11:02:04: 15000000 INFO @ Fri, 10 Dec 2021 11:02:05: 12000000 INFO @ Fri, 10 Dec 2021 11:02:05: 10000000 INFO @ Fri, 10 Dec 2021 11:02:13: 16000000 INFO @ Fri, 10 Dec 2021 11:02:14: 11000000 INFO @ Fri, 10 Dec 2021 11:02:15: 13000000 INFO @ Fri, 10 Dec 2021 11:02:22: 12000000 INFO @ Fri, 10 Dec 2021 11:02:23: 17000000 INFO @ Fri, 10 Dec 2021 11:02:24: 14000000 INFO @ Fri, 10 Dec 2021 11:02:31: 13000000 INFO @ Fri, 10 Dec 2021 11:02:32: 18000000 INFO @ Fri, 10 Dec 2021 11:02:34: 15000000 INFO @ Fri, 10 Dec 2021 11:02:39: 14000000 INFO @ Fri, 10 Dec 2021 11:02:42: 19000000 INFO @ Fri, 10 Dec 2021 11:02:44: 16000000 INFO @ Fri, 10 Dec 2021 11:02:48: 15000000 INFO @ Fri, 10 Dec 2021 11:02:51: 20000000 INFO @ Fri, 10 Dec 2021 11:02:53: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:02:56: 16000000 INFO @ Fri, 10 Dec 2021 11:03:01: 21000000 INFO @ Fri, 10 Dec 2021 11:03:03: 18000000 INFO @ Fri, 10 Dec 2021 11:03:04: 17000000 INFO @ Fri, 10 Dec 2021 11:03:11: 22000000 INFO @ Fri, 10 Dec 2021 11:03:12: 19000000 INFO @ Fri, 10 Dec 2021 11:03:13: 18000000 INFO @ Fri, 10 Dec 2021 11:03:21: 23000000 INFO @ Fri, 10 Dec 2021 11:03:21: 19000000 INFO @ Fri, 10 Dec 2021 11:03:22: 20000000 INFO @ Fri, 10 Dec 2021 11:03:29: 20000000 INFO @ Fri, 10 Dec 2021 11:03:30: 24000000 INFO @ Fri, 10 Dec 2021 11:03:31: 21000000 INFO @ Fri, 10 Dec 2021 11:03:34: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:03:34: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:03:34: #1 total tags in treatment: 11544219 INFO @ Fri, 10 Dec 2021 11:03:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:03:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:03:34: #1 tags after filtering in treatment: 10811790 INFO @ Fri, 10 Dec 2021 11:03:34: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:03:34: #1 finished! INFO @ Fri, 10 Dec 2021 11:03:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:03:34: #2 number of paired peaks: 292 WARNING @ Fri, 10 Dec 2021 11:03:34: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Fri, 10 Dec 2021 11:03:34: start model_add_line... INFO @ Fri, 10 Dec 2021 11:03:35: start X-correlation... INFO @ Fri, 10 Dec 2021 11:03:35: end of X-cor INFO @ Fri, 10 Dec 2021 11:03:35: #2 finished! INFO @ Fri, 10 Dec 2021 11:03:35: #2 predicted fragment length is 184 bps INFO @ Fri, 10 Dec 2021 11:03:35: #2 alternative fragment length(s) may be 184 bps INFO @ Fri, 10 Dec 2021 11:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.05_model.r WARNING @ Fri, 10 Dec 2021 11:03:35: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:03:35: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Fri, 10 Dec 2021 11:03:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:03:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:03:38: 21000000 INFO @ Fri, 10 Dec 2021 11:03:41: 22000000 INFO @ Fri, 10 Dec 2021 11:03:46: 22000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:03:51: 23000000 INFO @ Fri, 10 Dec 2021 11:03:55: 23000000 INFO @ Fri, 10 Dec 2021 11:03:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:04:00: 24000000 INFO @ Fri, 10 Dec 2021 11:04:03: 24000000 INFO @ Fri, 10 Dec 2021 11:04:03: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:04:03: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:04:03: #1 total tags in treatment: 11544219 INFO @ Fri, 10 Dec 2021 11:04:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:04:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:04:04: #1 tags after filtering in treatment: 10811790 INFO @ Fri, 10 Dec 2021 11:04:04: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:04:04: #1 finished! INFO @ Fri, 10 Dec 2021 11:04:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:04:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:04:04: #2 number of paired peaks: 292 WARNING @ Fri, 10 Dec 2021 11:04:04: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Fri, 10 Dec 2021 11:04:04: start model_add_line... INFO @ Fri, 10 Dec 2021 11:04:04: start X-correlation... INFO @ Fri, 10 Dec 2021 11:04:04: end of X-cor INFO @ Fri, 10 Dec 2021 11:04:04: #2 finished! INFO @ Fri, 10 Dec 2021 11:04:04: #2 predicted fragment length is 184 bps INFO @ Fri, 10 Dec 2021 11:04:04: #2 alternative fragment length(s) may be 184 bps INFO @ Fri, 10 Dec 2021 11:04:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.10_model.r WARNING @ Fri, 10 Dec 2021 11:04:04: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:04:04: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Fri, 10 Dec 2021 11:04:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:04:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:04:06: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:04:06: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:04:06: #1 total tags in treatment: 11544219 INFO @ Fri, 10 Dec 2021 11:04:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:04:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:04:06: #1 tags after filtering in treatment: 10811790 INFO @ Fri, 10 Dec 2021 11:04:06: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:04:06: #1 finished! INFO @ Fri, 10 Dec 2021 11:04:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:04:07: #2 number of paired peaks: 292 WARNING @ Fri, 10 Dec 2021 11:04:07: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Fri, 10 Dec 2021 11:04:07: start model_add_line... INFO @ Fri, 10 Dec 2021 11:04:07: start X-correlation... INFO @ Fri, 10 Dec 2021 11:04:07: end of X-cor INFO @ Fri, 10 Dec 2021 11:04:07: #2 finished! INFO @ Fri, 10 Dec 2021 11:04:07: #2 predicted fragment length is 184 bps INFO @ Fri, 10 Dec 2021 11:04:07: #2 alternative fragment length(s) may be 184 bps INFO @ Fri, 10 Dec 2021 11:04:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.20_model.r WARNING @ Fri, 10 Dec 2021 11:04:07: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:04:07: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Fri, 10 Dec 2021 11:04:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:04:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:04:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:04:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:04:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:04:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.05_summits.bed INFO @ Fri, 10 Dec 2021 11:04:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4101 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:04:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:04:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.10_summits.bed INFO @ Fri, 10 Dec 2021 11:04:37: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2046 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:04:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:04:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:04:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412056/SRX10412056.20_summits.bed INFO @ Fri, 10 Dec 2021 11:04:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (829 records, 4 fields): 2 millis CompletedMACS2peakCalling