Job ID = 14172042 SRX = SRX9103806 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23926170 spots for SRR12621006/SRR12621006.sra Written 23926170 spots for SRR12621006/SRR12621006.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172547 ("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: 00:22:10 23926170 reads; of these: 23926170 (100.00%) were paired; of these: 9354029 (39.10%) aligned concordantly 0 times 8466101 (35.38%) aligned concordantly exactly 1 time 6106040 (25.52%) aligned concordantly >1 times ---- 9354029 pairs aligned concordantly 0 times; of these: 1417312 (15.15%) aligned discordantly 1 time ---- 7936717 pairs aligned 0 times concordantly or discordantly; of these: 15873434 mates make up the pairs; of these: 13987535 (88.12%) aligned 0 times 530123 (3.34%) aligned exactly 1 time 1355776 (8.54%) aligned >1 times 70.77% overall alignment rate Time searching: 00:22:10 Overall time: 00:22:10 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 16 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] 4297283 / 15794231 = 0.2721 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 @ Sat, 11 Dec 2021 14:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.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, 11 Dec 2021 14:23:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:23:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:23:37: 1000000 INFO @ Sat, 11 Dec 2021 14:23:42: 2000000 INFO @ Sat, 11 Dec 2021 14:23:47: 3000000 INFO @ Sat, 11 Dec 2021 14:23:52: 4000000 INFO @ Sat, 11 Dec 2021 14:23:57: 5000000 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 @ Sat, 11 Dec 2021 14:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.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, 11 Dec 2021 14:24:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:24:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:24:02: 6000000 INFO @ Sat, 11 Dec 2021 14:24:07: 1000000 INFO @ Sat, 11 Dec 2021 14:24:07: 7000000 INFO @ Sat, 11 Dec 2021 14:24:12: 2000000 INFO @ Sat, 11 Dec 2021 14:24:12: 8000000 INFO @ Sat, 11 Dec 2021 14:24:17: 3000000 INFO @ Sat, 11 Dec 2021 14:24:18: 9000000 INFO @ Sat, 11 Dec 2021 14:24:22: 4000000 INFO @ Sat, 11 Dec 2021 14:24:23: 10000000 INFO @ Sat, 11 Dec 2021 14:24:27: 5000000 INFO @ Sat, 11 Dec 2021 14:24:28: 11000000 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 @ Sat, 11 Dec 2021 14:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.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, 11 Dec 2021 14:24:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:24:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:24:33: 6000000 INFO @ Sat, 11 Dec 2021 14:24:33: 12000000 INFO @ Sat, 11 Dec 2021 14:24:37: 1000000 INFO @ Sat, 11 Dec 2021 14:24:39: 7000000 INFO @ Sat, 11 Dec 2021 14:24:39: 13000000 INFO @ Sat, 11 Dec 2021 14:24:43: 2000000 INFO @ Sat, 11 Dec 2021 14:24:44: 8000000 INFO @ Sat, 11 Dec 2021 14:24:45: 14000000 INFO @ Sat, 11 Dec 2021 14:24:49: 3000000 INFO @ Sat, 11 Dec 2021 14:24:50: 9000000 INFO @ Sat, 11 Dec 2021 14:24:51: 15000000 INFO @ Sat, 11 Dec 2021 14:24:54: 4000000 INFO @ Sat, 11 Dec 2021 14:24:56: 10000000 INFO @ Sat, 11 Dec 2021 14:24:57: 16000000 INFO @ Sat, 11 Dec 2021 14:25:00: 5000000 INFO @ Sat, 11 Dec 2021 14:25:02: 11000000 INFO @ Sat, 11 Dec 2021 14:25:02: 17000000 INFO @ Sat, 11 Dec 2021 14:25:06: 6000000 INFO @ Sat, 11 Dec 2021 14:25:08: 12000000 INFO @ Sat, 11 Dec 2021 14:25:08: 18000000 INFO @ Sat, 11 Dec 2021 14:25:11: 7000000 INFO @ Sat, 11 Dec 2021 14:25:13: 13000000 INFO @ Sat, 11 Dec 2021 14:25:13: 19000000 INFO @ Sat, 11 Dec 2021 14:25:17: 8000000 INFO @ Sat, 11 Dec 2021 14:25:19: 14000000 INFO @ Sat, 11 Dec 2021 14:25:19: 20000000 INFO @ Sat, 11 Dec 2021 14:25:23: 9000000 INFO @ Sat, 11 Dec 2021 14:25:25: 15000000 INFO @ Sat, 11 Dec 2021 14:25:25: 21000000 INFO @ Sat, 11 Dec 2021 14:25:28: 10000000 INFO @ Sat, 11 Dec 2021 14:25:30: 16000000 INFO @ Sat, 11 Dec 2021 14:25:31: 22000000 INFO @ Sat, 11 Dec 2021 14:25:34: 11000000 INFO @ Sat, 11 Dec 2021 14:25:36: 17000000 INFO @ Sat, 11 Dec 2021 14:25:37: 23000000 INFO @ Sat, 11 Dec 2021 14:25:40: 12000000 INFO @ Sat, 11 Dec 2021 14:25:42: 18000000 INFO @ Sat, 11 Dec 2021 14:25:42: 24000000 INFO @ Sat, 11 Dec 2021 14:25:45: 13000000 INFO @ Sat, 11 Dec 2021 14:25:47: 19000000 INFO @ Sat, 11 Dec 2021 14:25:48: 25000000 INFO @ Sat, 11 Dec 2021 14:25:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:25:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:25:50: #1 total tags in treatment: 10385564 INFO @ Sat, 11 Dec 2021 14:25:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:25:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:25:50: #1 tags after filtering in treatment: 8112031 INFO @ Sat, 11 Dec 2021 14:25:50: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 14:25:50: #1 finished! INFO @ Sat, 11 Dec 2021 14:25:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:25:50: #2 number of paired peaks: 1150 INFO @ Sat, 11 Dec 2021 14:25:50: start model_add_line... INFO @ Sat, 11 Dec 2021 14:25:51: start X-correlation... INFO @ Sat, 11 Dec 2021 14:25:51: end of X-cor INFO @ Sat, 11 Dec 2021 14:25:51: #2 finished! INFO @ Sat, 11 Dec 2021 14:25:51: #2 predicted fragment length is 85 bps INFO @ Sat, 11 Dec 2021 14:25:51: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 11 Dec 2021 14:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.05_model.r WARNING @ Sat, 11 Dec 2021 14:25:51: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:25:51: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 11 Dec 2021 14:25:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:25:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:25:51: 14000000 INFO @ Sat, 11 Dec 2021 14:25:53: 20000000 INFO @ Sat, 11 Dec 2021 14:25:57: 15000000 INFO @ Sat, 11 Dec 2021 14:25:59: 21000000 INFO @ Sat, 11 Dec 2021 14:26:02: 16000000 INFO @ Sat, 11 Dec 2021 14:26:05: 22000000 INFO @ Sat, 11 Dec 2021 14:26:08: 17000000 INFO @ Sat, 11 Dec 2021 14:26:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:26:10: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:26:13: 18000000 INFO @ Sat, 11 Dec 2021 14:26:16: 24000000 INFO @ Sat, 11 Dec 2021 14:26:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:26:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:26:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.05_summits.bed INFO @ Sat, 11 Dec 2021 14:26:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9059 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:26:19: 19000000 INFO @ Sat, 11 Dec 2021 14:26:21: 25000000 INFO @ Sat, 11 Dec 2021 14:26:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:26:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:26:23: #1 total tags in treatment: 10385564 INFO @ Sat, 11 Dec 2021 14:26:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:26:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:26:23: #1 tags after filtering in treatment: 8112031 INFO @ Sat, 11 Dec 2021 14:26:23: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 14:26:23: #1 finished! INFO @ Sat, 11 Dec 2021 14:26:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:26:24: #2 number of paired peaks: 1150 INFO @ Sat, 11 Dec 2021 14:26:24: start model_add_line... INFO @ Sat, 11 Dec 2021 14:26:24: start X-correlation... INFO @ Sat, 11 Dec 2021 14:26:24: end of X-cor INFO @ Sat, 11 Dec 2021 14:26:24: #2 finished! INFO @ Sat, 11 Dec 2021 14:26:24: #2 predicted fragment length is 85 bps INFO @ Sat, 11 Dec 2021 14:26:24: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 11 Dec 2021 14:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.10_model.r WARNING @ Sat, 11 Dec 2021 14:26:24: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:26:24: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 11 Dec 2021 14:26:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:26:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:26:24: 20000000 INFO @ Sat, 11 Dec 2021 14:26:29: 21000000 INFO @ Sat, 11 Dec 2021 14:26:35: 22000000 INFO @ Sat, 11 Dec 2021 14:26:40: 23000000 INFO @ Sat, 11 Dec 2021 14:26:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:26:45: 24000000 INFO @ Sat, 11 Dec 2021 14:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.10_summits.bed INFO @ Sat, 11 Dec 2021 14:26:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4634 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:26:51: 25000000 INFO @ Sat, 11 Dec 2021 14:26:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:26:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:26:52: #1 total tags in treatment: 10385564 INFO @ Sat, 11 Dec 2021 14:26:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:26:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:26:52: #1 tags after filtering in treatment: 8112031 INFO @ Sat, 11 Dec 2021 14:26:52: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 14:26:52: #1 finished! INFO @ Sat, 11 Dec 2021 14:26:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:26:53: #2 number of paired peaks: 1150 INFO @ Sat, 11 Dec 2021 14:26:53: start model_add_line... INFO @ Sat, 11 Dec 2021 14:26:53: start X-correlation... INFO @ Sat, 11 Dec 2021 14:26:53: end of X-cor INFO @ Sat, 11 Dec 2021 14:26:53: #2 finished! INFO @ Sat, 11 Dec 2021 14:26:53: #2 predicted fragment length is 85 bps INFO @ Sat, 11 Dec 2021 14:26:53: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 11 Dec 2021 14:26:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.20_model.r WARNING @ Sat, 11 Dec 2021 14:26:53: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:26:53: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 11 Dec 2021 14:26:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:26:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:26:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:27:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103806/SRX9103806.20_summits.bed INFO @ Sat, 11 Dec 2021 14:27:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 3 millis CompletedMACS2peakCalling