Job ID = 14171981 SRX = SRX10089728 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25503277 spots for SRR13700615/SRR13700615.sra Written 25503277 spots for SRR13700615/SRR13700615.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172595 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:50:06 25503277 reads; of these: 25503277 (100.00%) were paired; of these: 5528097 (21.68%) aligned concordantly 0 times 15251289 (59.80%) aligned concordantly exactly 1 time 4723891 (18.52%) aligned concordantly >1 times ---- 5528097 pairs aligned concordantly 0 times; of these: 191997 (3.47%) aligned discordantly 1 time ---- 5336100 pairs aligned 0 times concordantly or discordantly; of these: 10672200 mates make up the pairs; of these: 9571947 (89.69%) aligned 0 times 590567 (5.53%) aligned exactly 1 time 509686 (4.78%) aligned >1 times 81.23% overall alignment rate Time searching: 00:50:07 Overall time: 00:50:07 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 20 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] 4952833 / 14013833 = 0.3534 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 14:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.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 14:44:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:44:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:44:39: 1000000 INFO @ Sat, 11 Dec 2021 14:44:45: 2000000 INFO @ Sat, 11 Dec 2021 14:44:50: 3000000 INFO @ Sat, 11 Dec 2021 14:44:56: 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 14:45:01: 5000000 INFO @ Sat, 11 Dec 2021 14:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.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 14:45:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:45:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:45:07: 6000000 INFO @ Sat, 11 Dec 2021 14:45:09: 1000000 INFO @ Sat, 11 Dec 2021 14:45:13: 7000000 INFO @ Sat, 11 Dec 2021 14:45:15: 2000000 INFO @ Sat, 11 Dec 2021 14:45:19: 8000000 INFO @ Sat, 11 Dec 2021 14:45:21: 3000000 INFO @ Sat, 11 Dec 2021 14:45:25: 9000000 INFO @ Sat, 11 Dec 2021 14:45:28: 4000000 INFO @ Sat, 11 Dec 2021 14:45:31: 10000000 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 14:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.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 14:45:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:45:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:45:34: 5000000 INFO @ Sat, 11 Dec 2021 14:45:37: 11000000 INFO @ Sat, 11 Dec 2021 14:45:41: 6000000 INFO @ Sat, 11 Dec 2021 14:45:41: 1000000 INFO @ Sat, 11 Dec 2021 14:45:43: 12000000 INFO @ Sat, 11 Dec 2021 14:45:48: 7000000 INFO @ Sat, 11 Dec 2021 14:45:48: 2000000 INFO @ Sat, 11 Dec 2021 14:45:49: 13000000 INFO @ Sat, 11 Dec 2021 14:45:54: 8000000 INFO @ Sat, 11 Dec 2021 14:45:56: 14000000 INFO @ Sat, 11 Dec 2021 14:45:56: 3000000 INFO @ Sat, 11 Dec 2021 14:46:00: 9000000 INFO @ Sat, 11 Dec 2021 14:46:02: 15000000 INFO @ Sat, 11 Dec 2021 14:46:03: 4000000 INFO @ Sat, 11 Dec 2021 14:46:07: 10000000 INFO @ Sat, 11 Dec 2021 14:46:08: 16000000 INFO @ Sat, 11 Dec 2021 14:46:10: 5000000 INFO @ Sat, 11 Dec 2021 14:46:13: 11000000 INFO @ Sat, 11 Dec 2021 14:46:14: 17000000 INFO @ Sat, 11 Dec 2021 14:46:17: 6000000 INFO @ Sat, 11 Dec 2021 14:46:19: 12000000 INFO @ Sat, 11 Dec 2021 14:46:20: 18000000 INFO @ Sat, 11 Dec 2021 14:46:25: 7000000 INFO @ Sat, 11 Dec 2021 14:46:26: 13000000 INFO @ Sat, 11 Dec 2021 14:46:27: 19000000 INFO @ Sat, 11 Dec 2021 14:46:32: 8000000 INFO @ Sat, 11 Dec 2021 14:46:32: 14000000 INFO @ Sat, 11 Dec 2021 14:46:33: 20000000 INFO @ Sat, 11 Dec 2021 14:46:38: 15000000 INFO @ Sat, 11 Dec 2021 14:46:39: 9000000 INFO @ Sat, 11 Dec 2021 14:46:39: 21000000 INFO @ Sat, 11 Dec 2021 14:46:45: 16000000 INFO @ Sat, 11 Dec 2021 14:46:46: 22000000 INFO @ Sat, 11 Dec 2021 14:46:46: 10000000 INFO @ Sat, 11 Dec 2021 14:46:51: 17000000 INFO @ Sat, 11 Dec 2021 14:46:52: 23000000 INFO @ Sat, 11 Dec 2021 14:46:54: 11000000 INFO @ Sat, 11 Dec 2021 14:46:57: 18000000 INFO @ Sat, 11 Dec 2021 14:46:59: 24000000 INFO @ Sat, 11 Dec 2021 14:47:01: 12000000 INFO @ Sat, 11 Dec 2021 14:47:04: 19000000 INFO @ Sat, 11 Dec 2021 14:47:05: 25000000 INFO @ Sat, 11 Dec 2021 14:47:08: 13000000 INFO @ Sat, 11 Dec 2021 14:47:11: 20000000 INFO @ Sat, 11 Dec 2021 14:47:12: 26000000 INFO @ Sat, 11 Dec 2021 14:47:15: 14000000 INFO @ Sat, 11 Dec 2021 14:47:17: 21000000 INFO @ Sat, 11 Dec 2021 14:47:18: 27000000 INFO @ Sat, 11 Dec 2021 14:47:23: 15000000 INFO @ Sat, 11 Dec 2021 14:47:24: 22000000 INFO @ Sat, 11 Dec 2021 14:47:24: 28000000 INFO @ Sat, 11 Dec 2021 14:47:30: 16000000 INFO @ Sat, 11 Dec 2021 14:47:30: 23000000 INFO @ Sat, 11 Dec 2021 14:47:31: 29000000 INFO @ Sat, 11 Dec 2021 14:47:37: 17000000 INFO @ Sat, 11 Dec 2021 14:47:37: 24000000 INFO @ Sat, 11 Dec 2021 14:47:37: 30000000 INFO @ Sat, 11 Dec 2021 14:47:43: 31000000 INFO @ Sat, 11 Dec 2021 14:47:43: 25000000 INFO @ Sat, 11 Dec 2021 14:47:44: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:47:47: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:47:47: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:47:47: #1 total tags in treatment: 15027300 INFO @ Sat, 11 Dec 2021 14:47:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:47:47: #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 14:47:47: #1 tags after filtering in treatment: 9006165 INFO @ Sat, 11 Dec 2021 14:47:47: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 11 Dec 2021 14:47:47: #1 finished! INFO @ Sat, 11 Dec 2021 14:47:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:47:48: #2 number of paired peaks: 2317 INFO @ Sat, 11 Dec 2021 14:47:48: start model_add_line... INFO @ Sat, 11 Dec 2021 14:47:48: start X-correlation... INFO @ Sat, 11 Dec 2021 14:47:48: end of X-cor INFO @ Sat, 11 Dec 2021 14:47:48: #2 finished! INFO @ Sat, 11 Dec 2021 14:47:48: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 14:47:48: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 11 Dec 2021 14:47:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.05_model.r WARNING @ Sat, 11 Dec 2021 14:47:48: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:47:48: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 11 Dec 2021 14:47:48: #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 14:47:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:47:50: 26000000 INFO @ Sat, 11 Dec 2021 14:47:51: 19000000 INFO @ Sat, 11 Dec 2021 14:47:57: 27000000 INFO @ Sat, 11 Dec 2021 14:47:58: 20000000 INFO @ Sat, 11 Dec 2021 14:48:04: 28000000 INFO @ Sat, 11 Dec 2021 14:48:06: 21000000 INFO @ Sat, 11 Dec 2021 14:48:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:48:10: 29000000 INFO @ Sat, 11 Dec 2021 14:48:13: 22000000 INFO @ Sat, 11 Dec 2021 14:48:17: 30000000 INFO @ Sat, 11 Dec 2021 14:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.05_peaks.xls BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.05_summits.bed INFO @ Sat, 11 Dec 2021 14:48:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (15534 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:48:20: 23000000 INFO @ Sat, 11 Dec 2021 14:48:23: 31000000 INFO @ Sat, 11 Dec 2021 14:48:27: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:48:27: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:48:27: #1 total tags in treatment: 15027300 INFO @ Sat, 11 Dec 2021 14:48:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:48:27: #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 14:48:27: #1 tags after filtering in treatment: 9006165 INFO @ Sat, 11 Dec 2021 14:48:27: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 11 Dec 2021 14:48:27: #1 finished! INFO @ Sat, 11 Dec 2021 14:48:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:48:28: 24000000 INFO @ Sat, 11 Dec 2021 14:48:28: #2 number of paired peaks: 2317 INFO @ Sat, 11 Dec 2021 14:48:28: start model_add_line... INFO @ Sat, 11 Dec 2021 14:48:28: start X-correlation... INFO @ Sat, 11 Dec 2021 14:48:28: end of X-cor INFO @ Sat, 11 Dec 2021 14:48:28: #2 finished! INFO @ Sat, 11 Dec 2021 14:48:28: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 14:48:28: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 11 Dec 2021 14:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.10_model.r WARNING @ Sat, 11 Dec 2021 14:48:28: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:48:28: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 11 Dec 2021 14:48:28: #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 14:48:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:48:35: 25000000 INFO @ Sat, 11 Dec 2021 14:48:42: 26000000 INFO @ Sat, 11 Dec 2021 14:48:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:48:49: 27000000 INFO @ Sat, 11 Dec 2021 14:48:56: 28000000 INFO @ Sat, 11 Dec 2021 14:48:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:48:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:48:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.10_summits.bed INFO @ Sat, 11 Dec 2021 14:48:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9436 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:49:03: 29000000 INFO @ Sat, 11 Dec 2021 14:49:10: 30000000 INFO @ Sat, 11 Dec 2021 14:49:17: 31000000 INFO @ Sat, 11 Dec 2021 14:49:21: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:49:21: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:49:21: #1 total tags in treatment: 15027300 INFO @ Sat, 11 Dec 2021 14:49:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:49:21: #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 14:49:21: #1 tags after filtering in treatment: 9006165 INFO @ Sat, 11 Dec 2021 14:49:21: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 11 Dec 2021 14:49:21: #1 finished! INFO @ Sat, 11 Dec 2021 14:49:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:49:22: #2 number of paired peaks: 2317 INFO @ Sat, 11 Dec 2021 14:49:22: start model_add_line... INFO @ Sat, 11 Dec 2021 14:49:22: start X-correlation... INFO @ Sat, 11 Dec 2021 14:49:22: end of X-cor INFO @ Sat, 11 Dec 2021 14:49:22: #2 finished! INFO @ Sat, 11 Dec 2021 14:49:22: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 14:49:22: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 11 Dec 2021 14:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.20_model.r WARNING @ Sat, 11 Dec 2021 14:49:22: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:49:22: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 11 Dec 2021 14:49:22: #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 14:49:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:49:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089728/SRX10089728.20_summits.bed INFO @ Sat, 11 Dec 2021 14:49:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4112 records, 4 fields): 6 millis CompletedMACS2peakCalling