Job ID = 16439375 SRX = SRX14232185 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21721868 spots for SRR18080633/SRR18080633.sra Written 21721868 spots for SRR18080633/SRR18080633.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440082 ("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: 01:46:33 21721868 reads; of these: 21721868 (100.00%) were paired; of these: 7140387 (32.87%) aligned concordantly 0 times 10757343 (49.52%) aligned concordantly exactly 1 time 3824138 (17.61%) aligned concordantly >1 times ---- 7140387 pairs aligned concordantly 0 times; of these: 3205696 (44.90%) aligned discordantly 1 time ---- 3934691 pairs aligned 0 times concordantly or discordantly; of these: 7869382 mates make up the pairs; of these: 5480076 (69.64%) aligned 0 times 457062 (5.81%) aligned exactly 1 time 1932244 (24.55%) aligned >1 times 87.39% overall alignment rate Time searching: 01:46:33 Overall time: 01:46:33 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 28 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] 3567079 / 17347932 = 0.2056 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 17:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.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 17:10:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:10:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:11:06: 1000000 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 17:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.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 17:11:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:11:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:11:22: 2000000 INFO @ Tue, 02 Aug 2022 17:11:35: 1000000 INFO @ Tue, 02 Aug 2022 17:11:38: 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 17:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.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 17:11:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:11:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:11:52: 2000000 INFO @ Tue, 02 Aug 2022 17:11:55: 4000000 INFO @ Tue, 02 Aug 2022 17:12:04: 1000000 INFO @ Tue, 02 Aug 2022 17:12:08: 3000000 INFO @ Tue, 02 Aug 2022 17:12:12: 5000000 INFO @ Tue, 02 Aug 2022 17:12:20: 2000000 INFO @ Tue, 02 Aug 2022 17:12:25: 4000000 INFO @ Tue, 02 Aug 2022 17:12:29: 6000000 INFO @ Tue, 02 Aug 2022 17:12:36: 3000000 INFO @ Tue, 02 Aug 2022 17:12:42: 5000000 INFO @ Tue, 02 Aug 2022 17:12:45: 7000000 INFO @ Tue, 02 Aug 2022 17:12:52: 4000000 INFO @ Tue, 02 Aug 2022 17:12:59: 6000000 INFO @ Tue, 02 Aug 2022 17:13:03: 8000000 INFO @ Tue, 02 Aug 2022 17:13:08: 5000000 INFO @ Tue, 02 Aug 2022 17:13:16: 7000000 INFO @ Tue, 02 Aug 2022 17:13:20: 9000000 INFO @ Tue, 02 Aug 2022 17:13:24: 6000000 INFO @ Tue, 02 Aug 2022 17:13:33: 8000000 INFO @ Tue, 02 Aug 2022 17:13:37: 10000000 INFO @ Tue, 02 Aug 2022 17:13:40: 7000000 INFO @ Tue, 02 Aug 2022 17:13:50: 9000000 INFO @ Tue, 02 Aug 2022 17:13:54: 11000000 INFO @ Tue, 02 Aug 2022 17:13:56: 8000000 INFO @ Tue, 02 Aug 2022 17:14:09: 10000000 INFO @ Tue, 02 Aug 2022 17:14:12: 12000000 INFO @ Tue, 02 Aug 2022 17:14:13: 9000000 INFO @ Tue, 02 Aug 2022 17:14:27: 11000000 INFO @ Tue, 02 Aug 2022 17:14:30: 10000000 INFO @ Tue, 02 Aug 2022 17:14:32: 13000000 INFO @ Tue, 02 Aug 2022 17:14:44: 12000000 INFO @ Tue, 02 Aug 2022 17:14:46: 11000000 INFO @ Tue, 02 Aug 2022 17:14:49: 14000000 INFO @ Tue, 02 Aug 2022 17:15:03: 13000000 INFO @ Tue, 02 Aug 2022 17:15:03: 12000000 INFO @ Tue, 02 Aug 2022 17:15:06: 15000000 INFO @ Tue, 02 Aug 2022 17:15:20: 13000000 INFO @ Tue, 02 Aug 2022 17:15:20: 14000000 INFO @ Tue, 02 Aug 2022 17:15:23: 16000000 INFO @ Tue, 02 Aug 2022 17:15:37: 15000000 INFO @ Tue, 02 Aug 2022 17:15:37: 14000000 INFO @ Tue, 02 Aug 2022 17:15:40: 17000000 INFO @ Tue, 02 Aug 2022 17:15:54: 15000000 INFO @ Tue, 02 Aug 2022 17:15:55: 16000000 INFO @ Tue, 02 Aug 2022 17:15:56: 18000000 INFO @ Tue, 02 Aug 2022 17:16:11: 16000000 INFO @ Tue, 02 Aug 2022 17:16:13: 17000000 INFO @ Tue, 02 Aug 2022 17:16:14: 19000000 INFO @ Tue, 02 Aug 2022 17:16:28: 17000000 INFO @ Tue, 02 Aug 2022 17:16:30: 18000000 INFO @ Tue, 02 Aug 2022 17:16:31: 20000000 INFO @ Tue, 02 Aug 2022 17:16:45: 18000000 INFO @ Tue, 02 Aug 2022 17:16:48: 19000000 INFO @ Tue, 02 Aug 2022 17:16:49: 21000000 INFO @ Tue, 02 Aug 2022 17:17:02: 19000000 INFO @ Tue, 02 Aug 2022 17:17:06: 20000000 INFO @ Tue, 02 Aug 2022 17:17:07: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:17:19: 20000000 INFO @ Tue, 02 Aug 2022 17:17:24: 21000000 INFO @ Tue, 02 Aug 2022 17:17:24: 23000000 INFO @ Tue, 02 Aug 2022 17:17:36: 21000000 INFO @ Tue, 02 Aug 2022 17:17:41: 24000000 INFO @ Tue, 02 Aug 2022 17:17:41: 22000000 INFO @ Tue, 02 Aug 2022 17:17:53: 22000000 INFO @ Tue, 02 Aug 2022 17:17:58: 25000000 INFO @ Tue, 02 Aug 2022 17:18:00: 23000000 INFO @ Tue, 02 Aug 2022 17:18:10: 23000000 INFO @ Tue, 02 Aug 2022 17:18:15: 26000000 INFO @ Tue, 02 Aug 2022 17:18:19: 24000000 INFO @ Tue, 02 Aug 2022 17:18:24: 24000000 INFO @ Tue, 02 Aug 2022 17:18:32: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:18:36: 25000000 INFO @ Tue, 02 Aug 2022 17:18:37: 25000000 INFO @ Tue, 02 Aug 2022 17:18:48: 28000000 INFO @ Tue, 02 Aug 2022 17:18:49: 26000000 INFO @ Tue, 02 Aug 2022 17:18:55: 26000000 INFO @ Tue, 02 Aug 2022 17:19:02: 27000000 INFO @ Tue, 02 Aug 2022 17:19:04: 29000000 INFO @ Tue, 02 Aug 2022 17:19:12: 27000000 INFO @ Tue, 02 Aug 2022 17:19:15: 28000000 INFO @ Tue, 02 Aug 2022 17:19:20: 30000000 INFO @ Tue, 02 Aug 2022 17:19:27: 29000000 INFO @ Tue, 02 Aug 2022 17:19:29: 28000000 INFO @ Tue, 02 Aug 2022 17:19:32: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:19:32: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:19:32: #1 total tags in treatment: 11624741 INFO @ Tue, 02 Aug 2022 17:19:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:19:32: #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 17:19:32: #1 tags after filtering in treatment: 10654978 INFO @ Tue, 02 Aug 2022 17:19:32: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 17:19:32: #1 finished! INFO @ Tue, 02 Aug 2022 17:19:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:19:33: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 17:19:33: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 02 Aug 2022 17:19:33: start model_add_line... INFO @ Tue, 02 Aug 2022 17:19:33: start X-correlation... INFO @ Tue, 02 Aug 2022 17:19:33: end of X-cor INFO @ Tue, 02 Aug 2022 17:19:33: #2 finished! INFO @ Tue, 02 Aug 2022 17:19:33: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 17:19:33: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 17:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.05_model.r WARNING @ Tue, 02 Aug 2022 17:19:33: #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 17:19:33: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 02 Aug 2022 17:19:33: #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 17:19:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:19:39: 30000000 INFO @ Tue, 02 Aug 2022 17:19:45: 29000000 INFO @ Tue, 02 Aug 2022 17:19:48: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:19:48: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:19:48: #1 total tags in treatment: 11624741 INFO @ Tue, 02 Aug 2022 17:19:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:19:48: #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 17:19:49: #1 tags after filtering in treatment: 10654978 INFO @ Tue, 02 Aug 2022 17:19:49: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 17:19:49: #1 finished! INFO @ Tue, 02 Aug 2022 17:19:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:19:49: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 17:19:49: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 02 Aug 2022 17:19:49: start model_add_line... INFO @ Tue, 02 Aug 2022 17:19:49: start X-correlation... INFO @ Tue, 02 Aug 2022 17:19:49: end of X-cor INFO @ Tue, 02 Aug 2022 17:19:49: #2 finished! INFO @ Tue, 02 Aug 2022 17:19:49: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 17:19:49: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 17:19:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.20_model.r WARNING @ Tue, 02 Aug 2022 17:19:50: #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 17:19:50: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 02 Aug 2022 17:19:50: #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 17:19:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:19:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:20:01: 30000000 INFO @ Tue, 02 Aug 2022 17:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.05_summits.bed INFO @ Tue, 02 Aug 2022 17:20:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1587 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:20:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:20:13: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:20:13: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:20:13: #1 total tags in treatment: 11624741 INFO @ Tue, 02 Aug 2022 17:20:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:20:13: #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 17:20:14: #1 tags after filtering in treatment: 10654978 INFO @ Tue, 02 Aug 2022 17:20:14: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 17:20:14: #1 finished! INFO @ Tue, 02 Aug 2022 17:20:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:20:14: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 17:20:14: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 02 Aug 2022 17:20:14: start model_add_line... INFO @ Tue, 02 Aug 2022 17:20:14: start X-correlation... INFO @ Tue, 02 Aug 2022 17:20:14: end of X-cor INFO @ Tue, 02 Aug 2022 17:20:14: #2 finished! INFO @ Tue, 02 Aug 2022 17:20:14: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 17:20:14: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 17:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.10_model.r WARNING @ Tue, 02 Aug 2022 17:20:14: #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 17:20:14: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Tue, 02 Aug 2022 17:20:14: #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 17:20:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.20_summits.bed INFO @ Tue, 02 Aug 2022 17:20:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:20:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232185/SRX14232185.10_summits.bed INFO @ Tue, 02 Aug 2022 17:20:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (843 records, 4 fields): 30 millis CompletedMACS2peakCalling