Job ID = 16439875 SRX = SRX12175821 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34313187 spots for SRR15884960/SRR15884960.sra Written 34313187 spots for SRR15884960/SRR15884960.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440733 ("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: 01:12:36 34313187 reads; of these: 34313187 (100.00%) were paired; of these: 19951685 (58.15%) aligned concordantly 0 times 12340249 (35.96%) aligned concordantly exactly 1 time 2021253 (5.89%) aligned concordantly >1 times ---- 19951685 pairs aligned concordantly 0 times; of these: 4488325 (22.50%) aligned discordantly 1 time ---- 15463360 pairs aligned 0 times concordantly or discordantly; of these: 30926720 mates make up the pairs; of these: 28348053 (91.66%) aligned 0 times 1360738 (4.40%) aligned exactly 1 time 1217929 (3.94%) aligned >1 times 58.69% overall alignment rate Time searching: 01:12:36 Overall time: 01:12:36 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 32 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] 3582559 / 18770306 = 0.1909 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 18:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.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 18:03:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:03:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:04:03: 1000000 INFO @ Tue, 02 Aug 2022 18:04:14: 2000000 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 18:04:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.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 18:04:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:04:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:04:24: 3000000 INFO @ Tue, 02 Aug 2022 18:04:35: 1000000 INFO @ Tue, 02 Aug 2022 18:04:37: 4000000 INFO @ Tue, 02 Aug 2022 18:04:48: 2000000 INFO @ Tue, 02 Aug 2022 18:04:48: 5000000 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 18:04:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.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 18:04:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:04:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:05:00: 6000000 INFO @ Tue, 02 Aug 2022 18:05:00: 3000000 INFO @ Tue, 02 Aug 2022 18:05:07: 1000000 INFO @ Tue, 02 Aug 2022 18:05:13: 7000000 INFO @ Tue, 02 Aug 2022 18:05:13: 4000000 INFO @ Tue, 02 Aug 2022 18:05:19: 2000000 INFO @ Tue, 02 Aug 2022 18:05:25: 8000000 INFO @ Tue, 02 Aug 2022 18:05:26: 5000000 INFO @ Tue, 02 Aug 2022 18:05:32: 3000000 INFO @ Tue, 02 Aug 2022 18:05:38: 6000000 INFO @ Tue, 02 Aug 2022 18:05:38: 9000000 INFO @ Tue, 02 Aug 2022 18:05:44: 4000000 INFO @ Tue, 02 Aug 2022 18:05:51: 7000000 INFO @ Tue, 02 Aug 2022 18:05:53: 10000000 INFO @ Tue, 02 Aug 2022 18:05:56: 5000000 INFO @ Tue, 02 Aug 2022 18:06:03: 8000000 INFO @ Tue, 02 Aug 2022 18:06:07: 11000000 INFO @ Tue, 02 Aug 2022 18:06:08: 6000000 INFO @ Tue, 02 Aug 2022 18:06:15: 9000000 INFO @ Tue, 02 Aug 2022 18:06:20: 12000000 INFO @ Tue, 02 Aug 2022 18:06:20: 7000000 INFO @ Tue, 02 Aug 2022 18:06:27: 10000000 INFO @ Tue, 02 Aug 2022 18:06:32: 8000000 INFO @ Tue, 02 Aug 2022 18:06:32: 13000000 INFO @ Tue, 02 Aug 2022 18:06:39: 11000000 INFO @ Tue, 02 Aug 2022 18:06:44: 9000000 INFO @ Tue, 02 Aug 2022 18:06:45: 14000000 INFO @ Tue, 02 Aug 2022 18:06:52: 12000000 INFO @ Tue, 02 Aug 2022 18:06:56: 10000000 INFO @ Tue, 02 Aug 2022 18:06:58: 15000000 INFO @ Tue, 02 Aug 2022 18:07:04: 13000000 INFO @ Tue, 02 Aug 2022 18:07:08: 11000000 INFO @ Tue, 02 Aug 2022 18:07:10: 16000000 INFO @ Tue, 02 Aug 2022 18:07:16: 14000000 INFO @ Tue, 02 Aug 2022 18:07:20: 12000000 INFO @ Tue, 02 Aug 2022 18:07:23: 17000000 INFO @ Tue, 02 Aug 2022 18:07:29: 15000000 INFO @ Tue, 02 Aug 2022 18:07:33: 13000000 INFO @ Tue, 02 Aug 2022 18:07:36: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:07:41: 16000000 INFO @ Tue, 02 Aug 2022 18:07:45: 14000000 INFO @ Tue, 02 Aug 2022 18:07:49: 19000000 INFO @ Tue, 02 Aug 2022 18:07:54: 17000000 INFO @ Tue, 02 Aug 2022 18:07:57: 15000000 INFO @ Tue, 02 Aug 2022 18:08:01: 20000000 INFO @ Tue, 02 Aug 2022 18:08:06: 18000000 INFO @ Tue, 02 Aug 2022 18:08:09: 16000000 INFO @ Tue, 02 Aug 2022 18:08:15: 21000000 INFO @ Tue, 02 Aug 2022 18:08:20: 19000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:08:22: 17000000 INFO @ Tue, 02 Aug 2022 18:08:27: 22000000 INFO @ Tue, 02 Aug 2022 18:08:32: 20000000 INFO @ Tue, 02 Aug 2022 18:08:34: 18000000 INFO @ Tue, 02 Aug 2022 18:08:39: 23000000 INFO @ Tue, 02 Aug 2022 18:08:43: 21000000 INFO @ Tue, 02 Aug 2022 18:08:47: 19000000 INFO @ Tue, 02 Aug 2022 18:08:52: 24000000 INFO @ Tue, 02 Aug 2022 18:08:55: 22000000 INFO @ Tue, 02 Aug 2022 18:08:59: 20000000 INFO @ Tue, 02 Aug 2022 18:09:05: 25000000 INFO @ Tue, 02 Aug 2022 18:09:08: 23000000 INFO @ Tue, 02 Aug 2022 18:09:11: 21000000 INFO @ Tue, 02 Aug 2022 18:09:17: 26000000 INFO @ Tue, 02 Aug 2022 18:09:20: 24000000 INFO @ Tue, 02 Aug 2022 18:09:23: 22000000 INFO @ Tue, 02 Aug 2022 18:09:29: 27000000 INFO @ Tue, 02 Aug 2022 18:09:33: 25000000 INFO @ Tue, 02 Aug 2022 18:09:35: 23000000 INFO @ Tue, 02 Aug 2022 18:09:41: 28000000 INFO @ Tue, 02 Aug 2022 18:09:45: 26000000 INFO @ Tue, 02 Aug 2022 18:09:47: 24000000 INFO @ Tue, 02 Aug 2022 18:09:54: 29000000 INFO @ Tue, 02 Aug 2022 18:09:57: 27000000 INFO @ Tue, 02 Aug 2022 18:09:58: 25000000 INFO @ Tue, 02 Aug 2022 18:10:06: 30000000 INFO @ Tue, 02 Aug 2022 18:10:09: 28000000 INFO @ Tue, 02 Aug 2022 18:10:10: 26000000 INFO @ Tue, 02 Aug 2022 18:10:18: 31000000 INFO @ Tue, 02 Aug 2022 18:10:21: 29000000 INFO @ Tue, 02 Aug 2022 18:10:22: 27000000 INFO @ Tue, 02 Aug 2022 18:10:30: 32000000 INFO @ Tue, 02 Aug 2022 18:10:33: 30000000 INFO @ Tue, 02 Aug 2022 18:10:34: 28000000 INFO @ Tue, 02 Aug 2022 18:10:43: 33000000 INFO @ Tue, 02 Aug 2022 18:10:44: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:10:44: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:10:44: #1 total tags in treatment: 11440730 INFO @ Tue, 02 Aug 2022 18:10:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:10:44: #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 18:10:45: #1 tags after filtering in treatment: 7198015 INFO @ Tue, 02 Aug 2022 18:10:45: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 02 Aug 2022 18:10:45: #1 finished! INFO @ Tue, 02 Aug 2022 18:10:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:10:45: 31000000 INFO @ Tue, 02 Aug 2022 18:10:45: #2 number of paired peaks: 4833 INFO @ Tue, 02 Aug 2022 18:10:45: start model_add_line... INFO @ Tue, 02 Aug 2022 18:10:46: start X-correlation... INFO @ Tue, 02 Aug 2022 18:10:46: end of X-cor INFO @ Tue, 02 Aug 2022 18:10:46: #2 finished! INFO @ Tue, 02 Aug 2022 18:10:46: #2 predicted fragment length is 246 bps INFO @ Tue, 02 Aug 2022 18:10:46: #2 alternative fragment length(s) may be 246 bps INFO @ Tue, 02 Aug 2022 18:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.05_model.r WARNING @ Tue, 02 Aug 2022 18:10:46: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:10:46: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Tue, 02 Aug 2022 18:10:46: #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 18:10:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:10:46: 29000000 INFO @ Tue, 02 Aug 2022 18:10:56: 32000000 INFO @ Tue, 02 Aug 2022 18:10:58: 30000000 INFO @ Tue, 02 Aug 2022 18:11:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:11:08: 33000000 INFO @ Tue, 02 Aug 2022 18:11:09: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:11:09: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:11:09: #1 total tags in treatment: 11440730 INFO @ Tue, 02 Aug 2022 18:11:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:11:09: #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 18:11:09: 31000000 INFO @ Tue, 02 Aug 2022 18:11:09: #1 tags after filtering in treatment: 7198015 INFO @ Tue, 02 Aug 2022 18:11:09: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 02 Aug 2022 18:11:09: #1 finished! INFO @ Tue, 02 Aug 2022 18:11:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:11:10: #2 number of paired peaks: 4833 INFO @ Tue, 02 Aug 2022 18:11:10: start model_add_line... INFO @ Tue, 02 Aug 2022 18:11:10: start X-correlation... INFO @ Tue, 02 Aug 2022 18:11:10: end of X-cor INFO @ Tue, 02 Aug 2022 18:11:10: #2 finished! INFO @ Tue, 02 Aug 2022 18:11:10: #2 predicted fragment length is 246 bps INFO @ Tue, 02 Aug 2022 18:11:10: #2 alternative fragment length(s) may be 246 bps INFO @ Tue, 02 Aug 2022 18:11:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.10_model.r WARNING @ Tue, 02 Aug 2022 18:11:10: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:11:10: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Tue, 02 Aug 2022 18:11:10: #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 18:11:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:11:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.05_summits.bed INFO @ Tue, 02 Aug 2022 18:11:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9811 records, 4 fields): 159 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:11:19: 32000000 INFO @ Tue, 02 Aug 2022 18:11:29: 33000000 INFO @ Tue, 02 Aug 2022 18:11:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:11:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:11:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:11:30: #1 total tags in treatment: 11440730 INFO @ Tue, 02 Aug 2022 18:11:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:11:30: #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 18:11:31: #1 tags after filtering in treatment: 7198015 INFO @ Tue, 02 Aug 2022 18:11:31: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 02 Aug 2022 18:11:31: #1 finished! INFO @ Tue, 02 Aug 2022 18:11:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:11:31: #2 number of paired peaks: 4833 INFO @ Tue, 02 Aug 2022 18:11:31: start model_add_line... INFO @ Tue, 02 Aug 2022 18:11:32: start X-correlation... INFO @ Tue, 02 Aug 2022 18:11:32: end of X-cor INFO @ Tue, 02 Aug 2022 18:11:32: #2 finished! INFO @ Tue, 02 Aug 2022 18:11:32: #2 predicted fragment length is 246 bps INFO @ Tue, 02 Aug 2022 18:11:32: #2 alternative fragment length(s) may be 246 bps INFO @ Tue, 02 Aug 2022 18:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.20_model.r WARNING @ Tue, 02 Aug 2022 18:11:32: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:11:32: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Tue, 02 Aug 2022 18:11:32: #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 18:11:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.10_summits.bed INFO @ Tue, 02 Aug 2022 18:11:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6980 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:11:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175821/SRX12175821.20_summits.bed INFO @ Tue, 02 Aug 2022 18:12:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3992 records, 4 fields): 36 millis CompletedMACS2peakCalling