Job ID = 14167196 SRX = SRX8913801 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24020474 spots for SRR12417800/SRR12417800.sra Written 24020474 spots for SRR12417800/SRR12417800.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168863 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 04:24:34 24020474 reads; of these: 24020474 (100.00%) were paired; of these: 7202231 (29.98%) aligned concordantly 0 times 4109195 (17.11%) aligned concordantly exactly 1 time 12709048 (52.91%) aligned concordantly >1 times ---- 7202231 pairs aligned concordantly 0 times; of these: 1014504 (14.09%) aligned discordantly 1 time ---- 6187727 pairs aligned 0 times concordantly or discordantly; of these: 12375454 mates make up the pairs; of these: 8173647 (66.05%) aligned 0 times 469654 (3.80%) aligned exactly 1 time 3732153 (30.16%) aligned >1 times 82.99% overall alignment rate Time searching: 04:24:35 Overall time: 04:24:35 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] 4969227 / 17519032 = 0.2836 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 @ Fri, 10 Dec 2021 15:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.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 @ Fri, 10 Dec 2021 15:40:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:40:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:40:19: 1000000 INFO @ Fri, 10 Dec 2021 15:40:27: 2000000 INFO @ Fri, 10 Dec 2021 15:40:36: 3000000 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 @ Fri, 10 Dec 2021 15:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.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 @ Fri, 10 Dec 2021 15:40:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:40:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:40:44: 4000000 INFO @ Fri, 10 Dec 2021 15:40:51: 1000000 INFO @ Fri, 10 Dec 2021 15:40:53: 5000000 INFO @ Fri, 10 Dec 2021 15:41:02: 2000000 INFO @ Fri, 10 Dec 2021 15:41:02: 6000000 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 @ Fri, 10 Dec 2021 15:41:11: 7000000 INFO @ Fri, 10 Dec 2021 15:41:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.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 @ Fri, 10 Dec 2021 15:41:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:41:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:41:12: 3000000 INFO @ Fri, 10 Dec 2021 15:41:21: 8000000 INFO @ Fri, 10 Dec 2021 15:41:21: 1000000 INFO @ Fri, 10 Dec 2021 15:41:23: 4000000 INFO @ Fri, 10 Dec 2021 15:41:30: 9000000 INFO @ Fri, 10 Dec 2021 15:41:30: 2000000 INFO @ Fri, 10 Dec 2021 15:41:33: 5000000 INFO @ Fri, 10 Dec 2021 15:41:39: 10000000 INFO @ Fri, 10 Dec 2021 15:41:40: 3000000 INFO @ Fri, 10 Dec 2021 15:41:44: 6000000 INFO @ Fri, 10 Dec 2021 15:41:49: 11000000 INFO @ Fri, 10 Dec 2021 15:41:49: 4000000 INFO @ Fri, 10 Dec 2021 15:41:55: 7000000 INFO @ Fri, 10 Dec 2021 15:41:58: 12000000 INFO @ Fri, 10 Dec 2021 15:41:59: 5000000 INFO @ Fri, 10 Dec 2021 15:42:05: 8000000 INFO @ Fri, 10 Dec 2021 15:42:08: 6000000 INFO @ Fri, 10 Dec 2021 15:42:08: 13000000 INFO @ Fri, 10 Dec 2021 15:42:16: 9000000 INFO @ Fri, 10 Dec 2021 15:42:17: 7000000 INFO @ Fri, 10 Dec 2021 15:42:18: 14000000 INFO @ Fri, 10 Dec 2021 15:42:26: 10000000 INFO @ Fri, 10 Dec 2021 15:42:27: 8000000 INFO @ Fri, 10 Dec 2021 15:42:27: 15000000 INFO @ Fri, 10 Dec 2021 15:42:36: 9000000 INFO @ Fri, 10 Dec 2021 15:42:37: 11000000 INFO @ Fri, 10 Dec 2021 15:42:37: 16000000 INFO @ Fri, 10 Dec 2021 15:42:46: 10000000 INFO @ Fri, 10 Dec 2021 15:42:47: 17000000 INFO @ Fri, 10 Dec 2021 15:42:48: 12000000 INFO @ Fri, 10 Dec 2021 15:42:55: 11000000 INFO @ Fri, 10 Dec 2021 15:42:56: 18000000 INFO @ Fri, 10 Dec 2021 15:42:59: 13000000 INFO @ Fri, 10 Dec 2021 15:43:04: 12000000 INFO @ Fri, 10 Dec 2021 15:43:06: 19000000 INFO @ Fri, 10 Dec 2021 15:43:10: 14000000 INFO @ Fri, 10 Dec 2021 15:43:14: 13000000 INFO @ Fri, 10 Dec 2021 15:43:15: 20000000 INFO @ Fri, 10 Dec 2021 15:43:20: 15000000 INFO @ Fri, 10 Dec 2021 15:43:24: 14000000 INFO @ Fri, 10 Dec 2021 15:43:25: 21000000 INFO @ Fri, 10 Dec 2021 15:43:31: 16000000 INFO @ Fri, 10 Dec 2021 15:43:33: 15000000 INFO @ Fri, 10 Dec 2021 15:43:34: 22000000 INFO @ Fri, 10 Dec 2021 15:43:42: 17000000 INFO @ Fri, 10 Dec 2021 15:43:43: 16000000 INFO @ Fri, 10 Dec 2021 15:43:44: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:43:53: 17000000 INFO @ Fri, 10 Dec 2021 15:43:53: 18000000 INFO @ Fri, 10 Dec 2021 15:43:53: 24000000 INFO @ Fri, 10 Dec 2021 15:44:02: 18000000 INFO @ Fri, 10 Dec 2021 15:44:03: 25000000 INFO @ Fri, 10 Dec 2021 15:44:03: 19000000 INFO @ Fri, 10 Dec 2021 15:44:11: 19000000 INFO @ Fri, 10 Dec 2021 15:44:13: 26000000 INFO @ Fri, 10 Dec 2021 15:44:14: 20000000 INFO @ Fri, 10 Dec 2021 15:44:21: 20000000 INFO @ Fri, 10 Dec 2021 15:44:23: 27000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:44:25: 21000000 INFO @ Fri, 10 Dec 2021 15:44:30: 21000000 INFO @ Fri, 10 Dec 2021 15:44:33: 28000000 INFO @ Fri, 10 Dec 2021 15:44:36: 22000000 INFO @ Fri, 10 Dec 2021 15:44:40: 22000000 INFO @ Fri, 10 Dec 2021 15:44:42: 29000000 INFO @ Fri, 10 Dec 2021 15:44:47: 23000000 INFO @ Fri, 10 Dec 2021 15:44:50: 23000000 INFO @ Fri, 10 Dec 2021 15:44:51: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 15:44:51: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 15:44:51: #1 total tags in treatment: 11944385 INFO @ Fri, 10 Dec 2021 15:44:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:44:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:44:51: #1 tags after filtering in treatment: 8395993 INFO @ Fri, 10 Dec 2021 15:44:51: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 10 Dec 2021 15:44:51: #1 finished! INFO @ Fri, 10 Dec 2021 15:44:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:44:52: #2 number of paired peaks: 3042 INFO @ Fri, 10 Dec 2021 15:44:52: start model_add_line... INFO @ Fri, 10 Dec 2021 15:44:52: start X-correlation... INFO @ Fri, 10 Dec 2021 15:44:52: end of X-cor INFO @ Fri, 10 Dec 2021 15:44:52: #2 finished! INFO @ Fri, 10 Dec 2021 15:44:52: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 15:44:52: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 15:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.05_model.r WARNING @ Fri, 10 Dec 2021 15:44:52: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:44:52: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Fri, 10 Dec 2021 15:44:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:44:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:44:58: 24000000 INFO @ Fri, 10 Dec 2021 15:45:00: 24000000 INFO @ Fri, 10 Dec 2021 15:45:10: 25000000 INFO @ Fri, 10 Dec 2021 15:45:10: 25000000 INFO @ Fri, 10 Dec 2021 15:45:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:45:21: 26000000 INFO @ Fri, 10 Dec 2021 15:45:22: 26000000 INFO @ Fri, 10 Dec 2021 15:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:45:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.05_summits.bed INFO @ Fri, 10 Dec 2021 15:45:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11136 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:45:33: 27000000 INFO @ Fri, 10 Dec 2021 15:45:34: 27000000 INFO @ Fri, 10 Dec 2021 15:45:45: 28000000 INFO @ Fri, 10 Dec 2021 15:45:45: 28000000 INFO @ Fri, 10 Dec 2021 15:45:56: 29000000 INFO @ Fri, 10 Dec 2021 15:45:57: 29000000 INFO @ Fri, 10 Dec 2021 15:46:06: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 15:46:06: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 15:46:06: #1 total tags in treatment: 11944385 INFO @ Fri, 10 Dec 2021 15:46:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:46:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:46:06: #1 tags after filtering in treatment: 8395993 INFO @ Fri, 10 Dec 2021 15:46:06: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 10 Dec 2021 15:46:06: #1 finished! INFO @ Fri, 10 Dec 2021 15:46:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:46:06: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 15:46:06: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 15:46:06: #1 total tags in treatment: 11944385 INFO @ Fri, 10 Dec 2021 15:46:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:46:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:46:07: #1 tags after filtering in treatment: 8395993 INFO @ Fri, 10 Dec 2021 15:46:07: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 10 Dec 2021 15:46:07: #1 finished! INFO @ Fri, 10 Dec 2021 15:46:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:46:07: #2 number of paired peaks: 3042 INFO @ Fri, 10 Dec 2021 15:46:07: start model_add_line... INFO @ Fri, 10 Dec 2021 15:46:07: start X-correlation... INFO @ Fri, 10 Dec 2021 15:46:07: end of X-cor INFO @ Fri, 10 Dec 2021 15:46:07: #2 finished! INFO @ Fri, 10 Dec 2021 15:46:07: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 15:46:07: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 15:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.10_model.r WARNING @ Fri, 10 Dec 2021 15:46:07: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:46:07: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Fri, 10 Dec 2021 15:46:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:46:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:46:07: #2 number of paired peaks: 3042 INFO @ Fri, 10 Dec 2021 15:46:07: start model_add_line... INFO @ Fri, 10 Dec 2021 15:46:08: start X-correlation... INFO @ Fri, 10 Dec 2021 15:46:08: end of X-cor INFO @ Fri, 10 Dec 2021 15:46:08: #2 finished! INFO @ Fri, 10 Dec 2021 15:46:08: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 15:46:08: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 15:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.20_model.r WARNING @ Fri, 10 Dec 2021 15:46:08: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:46:08: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Fri, 10 Dec 2021 15:46:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:46:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:46:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:46:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.10_summits.bed INFO @ Fri, 10 Dec 2021 15:46:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6976 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:46:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:46:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:46:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913801/SRX8913801.20_summits.bed INFO @ Fri, 10 Dec 2021 15:46:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3868 records, 4 fields): 5 millis CompletedMACS2peakCalling