Job ID = 16439349 SRX = SRX14232170 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18617299 spots for SRR18080648/SRR18080648.sra Written 18617299 spots for SRR18080648/SRR18080648.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439727 ("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: 00:59:54 18617299 reads; of these: 18617299 (100.00%) were paired; of these: 6408253 (34.42%) aligned concordantly 0 times 8855020 (47.56%) aligned concordantly exactly 1 time 3354026 (18.02%) aligned concordantly >1 times ---- 6408253 pairs aligned concordantly 0 times; of these: 2860449 (44.64%) aligned discordantly 1 time ---- 3547804 pairs aligned 0 times concordantly or discordantly; of these: 7095608 mates make up the pairs; of these: 4870474 (68.64%) aligned 0 times 430179 (6.06%) aligned exactly 1 time 1794955 (25.30%) aligned >1 times 86.92% overall alignment rate Time searching: 00:59:55 Overall time: 00:59:55 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] 2788630 / 14673885 = 0.1900 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:12:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.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 @ Tue, 02 Aug 2022 16:12:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:12:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:12:14: 1000000 INFO @ Tue, 02 Aug 2022 16:12:21: 2000000 INFO @ Tue, 02 Aug 2022 16:12:28: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:12:35: 4000000 INFO @ Tue, 02 Aug 2022 16:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.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 @ Tue, 02 Aug 2022 16:12:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:12:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:12:43: 5000000 INFO @ Tue, 02 Aug 2022 16:12:45: 1000000 INFO @ Tue, 02 Aug 2022 16:12:51: 6000000 INFO @ Tue, 02 Aug 2022 16:12:54: 2000000 INFO @ Tue, 02 Aug 2022 16:13:00: 7000000 INFO @ Tue, 02 Aug 2022 16:13:03: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.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 @ Tue, 02 Aug 2022 16:13:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:13:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:13:08: 8000000 INFO @ Tue, 02 Aug 2022 16:13:11: 4000000 INFO @ Tue, 02 Aug 2022 16:13:14: 1000000 INFO @ Tue, 02 Aug 2022 16:13:16: 9000000 INFO @ Tue, 02 Aug 2022 16:13:20: 5000000 INFO @ Tue, 02 Aug 2022 16:13:22: 2000000 INFO @ Tue, 02 Aug 2022 16:13:24: 10000000 INFO @ Tue, 02 Aug 2022 16:13:28: 6000000 INFO @ Tue, 02 Aug 2022 16:13:30: 3000000 INFO @ Tue, 02 Aug 2022 16:13:33: 11000000 INFO @ Tue, 02 Aug 2022 16:13:37: 7000000 INFO @ Tue, 02 Aug 2022 16:13:39: 4000000 INFO @ Tue, 02 Aug 2022 16:13:41: 12000000 INFO @ Tue, 02 Aug 2022 16:13:46: 8000000 INFO @ Tue, 02 Aug 2022 16:13:47: 5000000 INFO @ Tue, 02 Aug 2022 16:13:49: 13000000 INFO @ Tue, 02 Aug 2022 16:13:54: 9000000 INFO @ Tue, 02 Aug 2022 16:13:56: 6000000 INFO @ Tue, 02 Aug 2022 16:13:57: 14000000 INFO @ Tue, 02 Aug 2022 16:14:03: 10000000 INFO @ Tue, 02 Aug 2022 16:14:04: 7000000 INFO @ Tue, 02 Aug 2022 16:14:05: 15000000 INFO @ Tue, 02 Aug 2022 16:14:12: 11000000 INFO @ Tue, 02 Aug 2022 16:14:13: 16000000 INFO @ Tue, 02 Aug 2022 16:14:13: 8000000 INFO @ Tue, 02 Aug 2022 16:14:21: 12000000 INFO @ Tue, 02 Aug 2022 16:14:21: 17000000 INFO @ Tue, 02 Aug 2022 16:14:22: 9000000 INFO @ Tue, 02 Aug 2022 16:14:29: 18000000 INFO @ Tue, 02 Aug 2022 16:14:29: 13000000 INFO @ Tue, 02 Aug 2022 16:14:30: 10000000 INFO @ Tue, 02 Aug 2022 16:14:37: 19000000 INFO @ Tue, 02 Aug 2022 16:14:38: 14000000 INFO @ Tue, 02 Aug 2022 16:14:39: 11000000 INFO @ Tue, 02 Aug 2022 16:14:46: 20000000 INFO @ Tue, 02 Aug 2022 16:14:47: 15000000 INFO @ Tue, 02 Aug 2022 16:14:48: 12000000 INFO @ Tue, 02 Aug 2022 16:14:54: 21000000 INFO @ Tue, 02 Aug 2022 16:14:56: 16000000 INFO @ Tue, 02 Aug 2022 16:14:57: 13000000 INFO @ Tue, 02 Aug 2022 16:15:02: 22000000 INFO @ Tue, 02 Aug 2022 16:15:05: 17000000 INFO @ Tue, 02 Aug 2022 16:15:05: 14000000 INFO @ Tue, 02 Aug 2022 16:15:10: 23000000 INFO @ Tue, 02 Aug 2022 16:15:14: 15000000 INFO @ Tue, 02 Aug 2022 16:15:14: 18000000 INFO @ Tue, 02 Aug 2022 16:15:18: 24000000 INFO @ Tue, 02 Aug 2022 16:15:23: 16000000 INFO @ Tue, 02 Aug 2022 16:15:23: 19000000 INFO @ Tue, 02 Aug 2022 16:15:26: 25000000 INFO @ Tue, 02 Aug 2022 16:15:31: 17000000 INFO @ Tue, 02 Aug 2022 16:15:32: 20000000 INFO @ Tue, 02 Aug 2022 16:15:34: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:15:39: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:15:39: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:15:39: #1 total tags in treatment: 9912418 INFO @ Tue, 02 Aug 2022 16:15:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:15:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:15:40: #1 tags after filtering in treatment: 9139322 INFO @ Tue, 02 Aug 2022 16:15:40: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 16:15:40: #1 finished! INFO @ Tue, 02 Aug 2022 16:15:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:15:40: 18000000 INFO @ Tue, 02 Aug 2022 16:15:40: #2 number of paired peaks: 169 WARNING @ Tue, 02 Aug 2022 16:15:40: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 02 Aug 2022 16:15:40: start model_add_line... INFO @ Tue, 02 Aug 2022 16:15:40: start X-correlation... INFO @ Tue, 02 Aug 2022 16:15:40: end of X-cor INFO @ Tue, 02 Aug 2022 16:15:40: #2 finished! INFO @ Tue, 02 Aug 2022 16:15:40: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 16:15:40: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 16:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.05_model.r WARNING @ Tue, 02 Aug 2022 16:15:40: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:15:40: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 02 Aug 2022 16:15:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:15:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:15:41: 21000000 INFO @ Tue, 02 Aug 2022 16:15:48: 19000000 INFO @ Tue, 02 Aug 2022 16:15:50: 22000000 INFO @ Tue, 02 Aug 2022 16:15:57: 20000000 INFO @ Tue, 02 Aug 2022 16:15:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:15:59: 23000000 INFO @ Tue, 02 Aug 2022 16:16:05: 21000000 INFO @ Tue, 02 Aug 2022 16:16:08: 24000000 INFO @ Tue, 02 Aug 2022 16:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.05_summits.bed INFO @ Tue, 02 Aug 2022 16:16:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1590 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:16:14: 22000000 INFO @ Tue, 02 Aug 2022 16:16:16: 25000000 INFO @ Tue, 02 Aug 2022 16:16:23: 23000000 INFO @ Tue, 02 Aug 2022 16:16:25: 26000000 INFO @ Tue, 02 Aug 2022 16:16:31: 24000000 INFO @ Tue, 02 Aug 2022 16:16:32: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:16:32: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:16:32: #1 total tags in treatment: 9912418 INFO @ Tue, 02 Aug 2022 16:16:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:16:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:16:32: #1 tags after filtering in treatment: 9139322 INFO @ Tue, 02 Aug 2022 16:16:32: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 16:16:32: #1 finished! INFO @ Tue, 02 Aug 2022 16:16:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:16:32: #2 number of paired peaks: 169 WARNING @ Tue, 02 Aug 2022 16:16:32: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 02 Aug 2022 16:16:32: start model_add_line... INFO @ Tue, 02 Aug 2022 16:16:33: start X-correlation... INFO @ Tue, 02 Aug 2022 16:16:33: end of X-cor INFO @ Tue, 02 Aug 2022 16:16:33: #2 finished! INFO @ Tue, 02 Aug 2022 16:16:33: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 16:16:33: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 16:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.10_model.r WARNING @ Tue, 02 Aug 2022 16:16:33: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:16:33: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 02 Aug 2022 16:16:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:16:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:16:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:16:40: 25000000 INFO @ Tue, 02 Aug 2022 16:16:48: 26000000 INFO @ Tue, 02 Aug 2022 16:16:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:16:54: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:16:54: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:16:54: #1 total tags in treatment: 9912418 INFO @ Tue, 02 Aug 2022 16:16:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:16:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:16:54: #1 tags after filtering in treatment: 9139322 INFO @ Tue, 02 Aug 2022 16:16:54: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 16:16:54: #1 finished! INFO @ Tue, 02 Aug 2022 16:16:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:16:55: #2 number of paired peaks: 169 WARNING @ Tue, 02 Aug 2022 16:16:55: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 02 Aug 2022 16:16:55: start model_add_line... INFO @ Tue, 02 Aug 2022 16:16:55: start X-correlation... INFO @ Tue, 02 Aug 2022 16:16:55: end of X-cor INFO @ Tue, 02 Aug 2022 16:16:55: #2 finished! INFO @ Tue, 02 Aug 2022 16:16:55: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 16:16:55: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 16:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.20_model.r WARNING @ Tue, 02 Aug 2022 16:16:55: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:16:55: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 02 Aug 2022 16:16:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:16:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.10_summits.bed INFO @ Tue, 02 Aug 2022 16:17:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:17:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:17:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:17:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232170/SRX14232170.20_summits.bed INFO @ Tue, 02 Aug 2022 16:17:24: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (446 records, 4 fields): 81 millis CompletedMACS2peakCalling