Job ID = 14172041 SRX = SRX9103805 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24318499 spots for SRR12621005/SRR12621005.sra Written 24318499 spots for SRR12621005/SRR12621005.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172540 ("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: 00:20:06 24318499 reads; of these: 24318499 (100.00%) were paired; of these: 9782941 (40.23%) aligned concordantly 0 times 8165843 (33.58%) aligned concordantly exactly 1 time 6369715 (26.19%) aligned concordantly >1 times ---- 9782941 pairs aligned concordantly 0 times; of these: 1585195 (16.20%) aligned discordantly 1 time ---- 8197746 pairs aligned 0 times concordantly or discordantly; of these: 16395492 mates make up the pairs; of these: 14595953 (89.02%) aligned 0 times 577358 (3.52%) aligned exactly 1 time 1222181 (7.45%) aligned >1 times 69.99% overall alignment rate Time searching: 00:20:06 Overall time: 00:20:06 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] 4844702 / 15920907 = 0.3043 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 14:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.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 14:20:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:20:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:21:04: 1000000 INFO @ Sat, 11 Dec 2021 14:21:08: 2000000 INFO @ Sat, 11 Dec 2021 14:21:13: 3000000 INFO @ Sat, 11 Dec 2021 14:21:18: 4000000 INFO @ Sat, 11 Dec 2021 14:21:23: 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 14:21:28: 6000000 INFO @ Sat, 11 Dec 2021 14:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.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 14:21:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:21:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:21:33: 7000000 INFO @ Sat, 11 Dec 2021 14:21:34: 1000000 INFO @ Sat, 11 Dec 2021 14:21:38: 8000000 INFO @ Sat, 11 Dec 2021 14:21:39: 2000000 INFO @ Sat, 11 Dec 2021 14:21:43: 9000000 INFO @ Sat, 11 Dec 2021 14:21:44: 3000000 INFO @ Sat, 11 Dec 2021 14:21:49: 10000000 INFO @ Sat, 11 Dec 2021 14:21:50: 4000000 INFO @ Sat, 11 Dec 2021 14:21:54: 11000000 INFO @ Sat, 11 Dec 2021 14:21:55: 5000000 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 14:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.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 14:21:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:21:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:21:59: 12000000 INFO @ Sat, 11 Dec 2021 14:22:00: 6000000 INFO @ Sat, 11 Dec 2021 14:22:04: 1000000 INFO @ Sat, 11 Dec 2021 14:22:04: 13000000 INFO @ Sat, 11 Dec 2021 14:22:05: 7000000 INFO @ Sat, 11 Dec 2021 14:22:09: 2000000 INFO @ Sat, 11 Dec 2021 14:22:10: 14000000 INFO @ Sat, 11 Dec 2021 14:22:11: 8000000 INFO @ Sat, 11 Dec 2021 14:22:15: 3000000 INFO @ Sat, 11 Dec 2021 14:22:15: 15000000 INFO @ Sat, 11 Dec 2021 14:22:16: 9000000 INFO @ Sat, 11 Dec 2021 14:22:20: 4000000 INFO @ Sat, 11 Dec 2021 14:22:20: 16000000 INFO @ Sat, 11 Dec 2021 14:22:21: 10000000 INFO @ Sat, 11 Dec 2021 14:22:25: 5000000 INFO @ Sat, 11 Dec 2021 14:22:25: 17000000 INFO @ Sat, 11 Dec 2021 14:22:27: 11000000 INFO @ Sat, 11 Dec 2021 14:22:30: 6000000 INFO @ Sat, 11 Dec 2021 14:22:30: 18000000 INFO @ Sat, 11 Dec 2021 14:22:32: 12000000 INFO @ Sat, 11 Dec 2021 14:22:36: 19000000 INFO @ Sat, 11 Dec 2021 14:22:36: 7000000 INFO @ Sat, 11 Dec 2021 14:22:37: 13000000 INFO @ Sat, 11 Dec 2021 14:22:41: 8000000 INFO @ Sat, 11 Dec 2021 14:22:41: 20000000 INFO @ Sat, 11 Dec 2021 14:22:42: 14000000 INFO @ Sat, 11 Dec 2021 14:22:46: 9000000 INFO @ Sat, 11 Dec 2021 14:22:46: 21000000 INFO @ Sat, 11 Dec 2021 14:22:48: 15000000 INFO @ Sat, 11 Dec 2021 14:22:51: 10000000 INFO @ Sat, 11 Dec 2021 14:22:52: 22000000 INFO @ Sat, 11 Dec 2021 14:22:53: 16000000 INFO @ Sat, 11 Dec 2021 14:22:57: 11000000 INFO @ Sat, 11 Dec 2021 14:22:57: 23000000 INFO @ Sat, 11 Dec 2021 14:22:58: 17000000 INFO @ Sat, 11 Dec 2021 14:23:02: 12000000 INFO @ Sat, 11 Dec 2021 14:23:02: 24000000 INFO @ Sat, 11 Dec 2021 14:23:03: 18000000 INFO @ Sat, 11 Dec 2021 14:23:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:23:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:23:04: #1 total tags in treatment: 9851368 INFO @ Sat, 11 Dec 2021 14:23:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:23:04: #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 14:23:04: #1 tags after filtering in treatment: 7433430 INFO @ Sat, 11 Dec 2021 14:23:04: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 11 Dec 2021 14:23:04: #1 finished! INFO @ Sat, 11 Dec 2021 14:23:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:23:05: #2 number of paired peaks: 1798 INFO @ Sat, 11 Dec 2021 14:23:05: start model_add_line... INFO @ Sat, 11 Dec 2021 14:23:05: start X-correlation... INFO @ Sat, 11 Dec 2021 14:23:05: end of X-cor INFO @ Sat, 11 Dec 2021 14:23:05: #2 finished! INFO @ Sat, 11 Dec 2021 14:23:05: #2 predicted fragment length is 78 bps INFO @ Sat, 11 Dec 2021 14:23:05: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 11 Dec 2021 14:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.05_model.r WARNING @ Sat, 11 Dec 2021 14:23:05: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:23:05: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 11 Dec 2021 14:23:05: #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 14:23:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:23:07: 13000000 INFO @ Sat, 11 Dec 2021 14:23:08: 19000000 INFO @ Sat, 11 Dec 2021 14:23:12: 14000000 INFO @ Sat, 11 Dec 2021 14:23:13: 20000000 INFO @ Sat, 11 Dec 2021 14:23:17: 15000000 INFO @ Sat, 11 Dec 2021 14:23:19: 21000000 INFO @ Sat, 11 Dec 2021 14:23:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:23:22: 16000000 INFO @ Sat, 11 Dec 2021 14:23:24: 22000000 INFO @ Sat, 11 Dec 2021 14:23:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:23:28: 17000000 INFO @ Sat, 11 Dec 2021 14:23:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:23:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.05_summits.bed INFO @ Sat, 11 Dec 2021 14:23:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9935 records, 4 fields): 89 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:23:29: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:23:33: 18000000 INFO @ Sat, 11 Dec 2021 14:23:34: 24000000 INFO @ Sat, 11 Dec 2021 14:23:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:23:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:23:36: #1 total tags in treatment: 9851368 INFO @ Sat, 11 Dec 2021 14:23:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:23:36: #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 14:23:36: #1 tags after filtering in treatment: 7433430 INFO @ Sat, 11 Dec 2021 14:23:36: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 11 Dec 2021 14:23:36: #1 finished! INFO @ Sat, 11 Dec 2021 14:23:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:23:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:23:37: #2 number of paired peaks: 1798 INFO @ Sat, 11 Dec 2021 14:23:37: start model_add_line... INFO @ Sat, 11 Dec 2021 14:23:37: start X-correlation... INFO @ Sat, 11 Dec 2021 14:23:37: end of X-cor INFO @ Sat, 11 Dec 2021 14:23:37: #2 finished! INFO @ Sat, 11 Dec 2021 14:23:37: #2 predicted fragment length is 78 bps INFO @ Sat, 11 Dec 2021 14:23:37: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 11 Dec 2021 14:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.10_model.r WARNING @ Sat, 11 Dec 2021 14:23:37: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:23:37: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 11 Dec 2021 14:23:37: #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 14:23:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:23:38: 19000000 INFO @ Sat, 11 Dec 2021 14:23:43: 20000000 INFO @ Sat, 11 Dec 2021 14:23:48: 21000000 INFO @ Sat, 11 Dec 2021 14:23:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:23:53: 22000000 INFO @ Sat, 11 Dec 2021 14:23:58: 23000000 INFO @ Sat, 11 Dec 2021 14:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:24:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:24:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.10_summits.bed INFO @ Sat, 11 Dec 2021 14:24:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5362 records, 4 fields): 110 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:24:03: 24000000 INFO @ Sat, 11 Dec 2021 14:24:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:24:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:24:05: #1 total tags in treatment: 9851368 INFO @ Sat, 11 Dec 2021 14:24:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:24:05: #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 14:24:05: #1 tags after filtering in treatment: 7433430 INFO @ Sat, 11 Dec 2021 14:24:05: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 11 Dec 2021 14:24:05: #1 finished! INFO @ Sat, 11 Dec 2021 14:24:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:24:05: #2 number of paired peaks: 1798 INFO @ Sat, 11 Dec 2021 14:24:05: start model_add_line... INFO @ Sat, 11 Dec 2021 14:24:05: start X-correlation... INFO @ Sat, 11 Dec 2021 14:24:05: end of X-cor INFO @ Sat, 11 Dec 2021 14:24:05: #2 finished! INFO @ Sat, 11 Dec 2021 14:24:05: #2 predicted fragment length is 78 bps INFO @ Sat, 11 Dec 2021 14:24:05: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 11 Dec 2021 14:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.20_model.r WARNING @ Sat, 11 Dec 2021 14:24:05: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:24:05: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 11 Dec 2021 14:24:05: #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 14:24:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:24:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:24:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103805/SRX9103805.20_summits.bed INFO @ Sat, 11 Dec 2021 14:24:27: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1417 records, 4 fields): 3 millis CompletedMACS2peakCalling