Job ID = 14169701 SRX = ERX3978784 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24033400 spots for ERR3975809/ERR3975809.sra Written 24033400 spots for ERR3975809/ERR3975809.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170571 ("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: 00:50:17 24033400 reads; of these: 24033400 (100.00%) were paired; of these: 8459916 (35.20%) aligned concordantly 0 times 7994394 (33.26%) aligned concordantly exactly 1 time 7579090 (31.54%) aligned concordantly >1 times ---- 8459916 pairs aligned concordantly 0 times; of these: 2541105 (30.04%) aligned discordantly 1 time ---- 5918811 pairs aligned 0 times concordantly or discordantly; of these: 11837622 mates make up the pairs; of these: 7347696 (62.07%) aligned 0 times 463955 (3.92%) aligned exactly 1 time 4025971 (34.01%) aligned >1 times 84.71% overall alignment rate Time searching: 00:50:17 Overall time: 00:50:17 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] 5732167 / 18009833 = 0.3183 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 04:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.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 04:16:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:16:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:16:26: 1000000 INFO @ Sat, 11 Dec 2021 04:16:33: 2000000 INFO @ Sat, 11 Dec 2021 04:16:40: 3000000 INFO @ Sat, 11 Dec 2021 04:16:46: 4000000 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 04:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.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 04:16:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:16:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:16:54: 5000000 INFO @ Sat, 11 Dec 2021 04:16:58: 1000000 INFO @ Sat, 11 Dec 2021 04:17:01: 6000000 INFO @ Sat, 11 Dec 2021 04:17:06: 2000000 INFO @ Sat, 11 Dec 2021 04:17:09: 7000000 INFO @ Sat, 11 Dec 2021 04:17:14: 3000000 INFO @ Sat, 11 Dec 2021 04:17:17: 8000000 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 04:17:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.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 04:17:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:17:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:17:22: 4000000 INFO @ Sat, 11 Dec 2021 04:17:25: 9000000 INFO @ Sat, 11 Dec 2021 04:17:27: 1000000 INFO @ Sat, 11 Dec 2021 04:17:31: 5000000 INFO @ Sat, 11 Dec 2021 04:17:33: 10000000 INFO @ Sat, 11 Dec 2021 04:17:35: 2000000 INFO @ Sat, 11 Dec 2021 04:17:39: 6000000 INFO @ Sat, 11 Dec 2021 04:17:41: 11000000 INFO @ Sat, 11 Dec 2021 04:17:43: 3000000 INFO @ Sat, 11 Dec 2021 04:17:47: 7000000 INFO @ Sat, 11 Dec 2021 04:17:49: 12000000 INFO @ Sat, 11 Dec 2021 04:17:51: 4000000 INFO @ Sat, 11 Dec 2021 04:17:55: 8000000 INFO @ Sat, 11 Dec 2021 04:17:57: 13000000 INFO @ Sat, 11 Dec 2021 04:17:59: 5000000 INFO @ Sat, 11 Dec 2021 04:18:04: 9000000 INFO @ Sat, 11 Dec 2021 04:18:05: 14000000 INFO @ Sat, 11 Dec 2021 04:18:07: 6000000 INFO @ Sat, 11 Dec 2021 04:18:12: 10000000 INFO @ Sat, 11 Dec 2021 04:18:13: 15000000 INFO @ Sat, 11 Dec 2021 04:18:15: 7000000 INFO @ Sat, 11 Dec 2021 04:18:20: 11000000 INFO @ Sat, 11 Dec 2021 04:18:21: 16000000 INFO @ Sat, 11 Dec 2021 04:18:23: 8000000 INFO @ Sat, 11 Dec 2021 04:18:28: 17000000 INFO @ Sat, 11 Dec 2021 04:18:29: 12000000 INFO @ Sat, 11 Dec 2021 04:18:31: 9000000 INFO @ Sat, 11 Dec 2021 04:18:36: 18000000 INFO @ Sat, 11 Dec 2021 04:18:37: 13000000 INFO @ Sat, 11 Dec 2021 04:18:39: 10000000 INFO @ Sat, 11 Dec 2021 04:18:44: 19000000 INFO @ Sat, 11 Dec 2021 04:18:45: 14000000 INFO @ Sat, 11 Dec 2021 04:18:47: 11000000 INFO @ Sat, 11 Dec 2021 04:18:51: 20000000 INFO @ Sat, 11 Dec 2021 04:18:53: 15000000 INFO @ Sat, 11 Dec 2021 04:18:55: 12000000 INFO @ Sat, 11 Dec 2021 04:18:59: 21000000 INFO @ Sat, 11 Dec 2021 04:19:02: 16000000 INFO @ Sat, 11 Dec 2021 04:19:03: 13000000 INFO @ Sat, 11 Dec 2021 04:19:07: 22000000 INFO @ Sat, 11 Dec 2021 04:19:10: 17000000 INFO @ Sat, 11 Dec 2021 04:19:11: 14000000 INFO @ Sat, 11 Dec 2021 04:19:15: 23000000 INFO @ Sat, 11 Dec 2021 04:19:18: 18000000 INFO @ Sat, 11 Dec 2021 04:19:19: 15000000 INFO @ Sat, 11 Dec 2021 04:19:23: 24000000 INFO @ Sat, 11 Dec 2021 04:19:26: 19000000 INFO @ Sat, 11 Dec 2021 04:19:26: 16000000 INFO @ Sat, 11 Dec 2021 04:19:31: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 04:19:34: 20000000 INFO @ Sat, 11 Dec 2021 04:19:35: 17000000 INFO @ Sat, 11 Dec 2021 04:19:39: 26000000 INFO @ Sat, 11 Dec 2021 04:19:42: 21000000 INFO @ Sat, 11 Dec 2021 04:19:43: 18000000 INFO @ Sat, 11 Dec 2021 04:19:47: 27000000 INFO @ Sat, 11 Dec 2021 04:19:50: 22000000 INFO @ Sat, 11 Dec 2021 04:19:51: 19000000 INFO @ Sat, 11 Dec 2021 04:19:56: 28000000 INFO @ Sat, 11 Dec 2021 04:19:58: 23000000 INFO @ Sat, 11 Dec 2021 04:19:59: 20000000 INFO @ Sat, 11 Dec 2021 04:20:04: 29000000 INFO @ Sat, 11 Dec 2021 04:20:06: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 04:20:06: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 04:20:06: #1 total tags in treatment: 9973420 INFO @ Sat, 11 Dec 2021 04:20:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 04:20:06: #1 tags after filtering in treatment: 7077800 INFO @ Sat, 11 Dec 2021 04:20:06: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 11 Dec 2021 04:20:06: #1 finished! INFO @ Sat, 11 Dec 2021 04:20:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:20:06: 24000000 INFO @ Sat, 11 Dec 2021 04:20:07: #2 number of paired peaks: 3478 INFO @ Sat, 11 Dec 2021 04:20:07: start model_add_line... INFO @ Sat, 11 Dec 2021 04:20:07: start X-correlation... INFO @ Sat, 11 Dec 2021 04:20:07: end of X-cor INFO @ Sat, 11 Dec 2021 04:20:07: #2 finished! INFO @ Sat, 11 Dec 2021 04:20:07: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 04:20:07: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 11 Dec 2021 04:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.05_model.r WARNING @ Sat, 11 Dec 2021 04:20:07: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:20:07: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 11 Dec 2021 04:20:07: #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 04:20:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:20:07: 21000000 INFO @ Sat, 11 Dec 2021 04:20:14: 25000000 INFO @ Sat, 11 Dec 2021 04:20:15: 22000000 INFO @ Sat, 11 Dec 2021 04:20:22: 26000000 INFO @ Sat, 11 Dec 2021 04:20:22: 23000000 INFO @ Sat, 11 Dec 2021 04:20:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:20:30: 24000000 INFO @ Sat, 11 Dec 2021 04:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.05_peaks.xls INFO @ Sat, 11 Dec 2021 04:20:30: 27000000 INFO @ Sat, 11 Dec 2021 04:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:20:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.05_summits.bed INFO @ Sat, 11 Dec 2021 04:20:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13458 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 04:20:38: 25000000 INFO @ Sat, 11 Dec 2021 04:20:38: 28000000 INFO @ Sat, 11 Dec 2021 04:20:46: 26000000 INFO @ Sat, 11 Dec 2021 04:20:46: 29000000 INFO @ Sat, 11 Dec 2021 04:20:48: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 04:20:48: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 04:20:48: #1 total tags in treatment: 9973420 INFO @ Sat, 11 Dec 2021 04:20:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:20:48: #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 04:20:49: #1 tags after filtering in treatment: 7077800 INFO @ Sat, 11 Dec 2021 04:20:49: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 11 Dec 2021 04:20:49: #1 finished! INFO @ Sat, 11 Dec 2021 04:20:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:20:49: #2 number of paired peaks: 3478 INFO @ Sat, 11 Dec 2021 04:20:49: start model_add_line... INFO @ Sat, 11 Dec 2021 04:20:49: start X-correlation... INFO @ Sat, 11 Dec 2021 04:20:49: end of X-cor INFO @ Sat, 11 Dec 2021 04:20:49: #2 finished! INFO @ Sat, 11 Dec 2021 04:20:49: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 04:20:49: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 11 Dec 2021 04:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.10_model.r WARNING @ Sat, 11 Dec 2021 04:20:49: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:20:49: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 11 Dec 2021 04:20:49: #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 04:20:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:20:54: 27000000 INFO @ Sat, 11 Dec 2021 04:21:01: 28000000 INFO @ Sat, 11 Dec 2021 04:21:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:21:09: 29000000 INFO @ Sat, 11 Dec 2021 04:21:10: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 04:21:10: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 04:21:10: #1 total tags in treatment: 9973420 INFO @ Sat, 11 Dec 2021 04:21:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:21:10: #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 04:21:11: #1 tags after filtering in treatment: 7077800 INFO @ Sat, 11 Dec 2021 04:21:11: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 11 Dec 2021 04:21:11: #1 finished! INFO @ Sat, 11 Dec 2021 04:21:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:21:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:21:11: #2 number of paired peaks: 3478 INFO @ Sat, 11 Dec 2021 04:21:11: start model_add_line... INFO @ Sat, 11 Dec 2021 04:21:11: start X-correlation... INFO @ Sat, 11 Dec 2021 04:21:11: end of X-cor INFO @ Sat, 11 Dec 2021 04:21:11: #2 finished! INFO @ Sat, 11 Dec 2021 04:21:11: #2 predicted fragment length is 210 bps INFO @ Sat, 11 Dec 2021 04:21:11: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 11 Dec 2021 04:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.20_model.r WARNING @ Sat, 11 Dec 2021 04:21:11: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:21:11: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 11 Dec 2021 04:21:11: #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 04:21:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.10_peaks.xls INFO @ Sat, 11 Dec 2021 04:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.10_summits.bed INFO @ Sat, 11 Dec 2021 04:21:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8642 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 04:21:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.20_peaks.xls INFO @ Sat, 11 Dec 2021 04:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978784/ERX3978784.20_summits.bed INFO @ Sat, 11 Dec 2021 04:21:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4047 records, 4 fields): 6 millis CompletedMACS2peakCalling