Job ID = 14172038 SRX = SRX9103803 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23094790 spots for SRR12621003/SRR12621003.sra Written 23094790 spots for SRR12621003/SRR12621003.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172535 ("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: 00:20:01 23094790 reads; of these: 23094790 (100.00%) were paired; of these: 6350515 (27.50%) aligned concordantly 0 times 8592642 (37.21%) aligned concordantly exactly 1 time 8151633 (35.30%) aligned concordantly >1 times ---- 6350515 pairs aligned concordantly 0 times; of these: 1308623 (20.61%) aligned discordantly 1 time ---- 5041892 pairs aligned 0 times concordantly or discordantly; of these: 10083784 mates make up the pairs; of these: 8417687 (83.48%) aligned 0 times 478438 (4.74%) aligned exactly 1 time 1187659 (11.78%) aligned >1 times 81.78% overall alignment rate Time searching: 00:20:01 Overall time: 00:20:01 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] 6618231 / 17877769 = 0.3702 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 14:20:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.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 14:20:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:20:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:20:23: 1000000 INFO @ Sat, 11 Dec 2021 14:20:29: 2000000 INFO @ Sat, 11 Dec 2021 14:20:35: 3000000 INFO @ Sat, 11 Dec 2021 14:20:41: 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 14:20:47: 5000000 INFO @ Sat, 11 Dec 2021 14:20:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.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 14:20:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:20:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:20:53: 6000000 INFO @ Sat, 11 Dec 2021 14:20:53: 1000000 INFO @ Sat, 11 Dec 2021 14:21:00: 7000000 INFO @ Sat, 11 Dec 2021 14:21:00: 2000000 INFO @ Sat, 11 Dec 2021 14:21:06: 3000000 INFO @ Sat, 11 Dec 2021 14:21:06: 8000000 INFO @ Sat, 11 Dec 2021 14:21:12: 4000000 INFO @ Sat, 11 Dec 2021 14:21:13: 9000000 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 14:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.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 14:21:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:21:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:21:18: 5000000 INFO @ Sat, 11 Dec 2021 14:21:19: 10000000 INFO @ Sat, 11 Dec 2021 14:21:23: 1000000 INFO @ Sat, 11 Dec 2021 14:21:24: 6000000 INFO @ Sat, 11 Dec 2021 14:21:26: 11000000 INFO @ Sat, 11 Dec 2021 14:21:30: 2000000 INFO @ Sat, 11 Dec 2021 14:21:30: 7000000 INFO @ Sat, 11 Dec 2021 14:21:32: 12000000 INFO @ Sat, 11 Dec 2021 14:21:36: 3000000 INFO @ Sat, 11 Dec 2021 14:21:37: 8000000 INFO @ Sat, 11 Dec 2021 14:21:38: 13000000 INFO @ Sat, 11 Dec 2021 14:21:42: 4000000 INFO @ Sat, 11 Dec 2021 14:21:43: 9000000 INFO @ Sat, 11 Dec 2021 14:21:45: 14000000 INFO @ Sat, 11 Dec 2021 14:21:49: 5000000 INFO @ Sat, 11 Dec 2021 14:21:49: 10000000 INFO @ Sat, 11 Dec 2021 14:21:51: 15000000 INFO @ Sat, 11 Dec 2021 14:21:55: 6000000 INFO @ Sat, 11 Dec 2021 14:21:55: 11000000 INFO @ Sat, 11 Dec 2021 14:21:58: 16000000 INFO @ Sat, 11 Dec 2021 14:22:01: 7000000 INFO @ Sat, 11 Dec 2021 14:22:02: 12000000 INFO @ Sat, 11 Dec 2021 14:22:04: 17000000 INFO @ Sat, 11 Dec 2021 14:22:08: 8000000 INFO @ Sat, 11 Dec 2021 14:22:08: 13000000 INFO @ Sat, 11 Dec 2021 14:22:10: 18000000 INFO @ Sat, 11 Dec 2021 14:22:14: 9000000 INFO @ Sat, 11 Dec 2021 14:22:15: 14000000 INFO @ Sat, 11 Dec 2021 14:22:16: 19000000 INFO @ Sat, 11 Dec 2021 14:22:21: 10000000 INFO @ Sat, 11 Dec 2021 14:22:21: 15000000 INFO @ Sat, 11 Dec 2021 14:22:22: 20000000 INFO @ Sat, 11 Dec 2021 14:22:27: 11000000 INFO @ Sat, 11 Dec 2021 14:22:27: 16000000 INFO @ Sat, 11 Dec 2021 14:22:29: 21000000 INFO @ Sat, 11 Dec 2021 14:22:33: 12000000 INFO @ Sat, 11 Dec 2021 14:22:33: 17000000 INFO @ Sat, 11 Dec 2021 14:22:35: 22000000 INFO @ Sat, 11 Dec 2021 14:22:40: 13000000 INFO @ Sat, 11 Dec 2021 14:22:40: 18000000 INFO @ Sat, 11 Dec 2021 14:22:41: 23000000 INFO @ Sat, 11 Dec 2021 14:22:46: 19000000 INFO @ Sat, 11 Dec 2021 14:22:46: 14000000 INFO @ Sat, 11 Dec 2021 14:22:48: 24000000 INFO @ Sat, 11 Dec 2021 14:22:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:22:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:22:51: #1 total tags in treatment: 10262821 INFO @ Sat, 11 Dec 2021 14:22:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:22:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:22:51: #1 tags after filtering in treatment: 7441080 INFO @ Sat, 11 Dec 2021 14:22:51: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 11 Dec 2021 14:22:51: #1 finished! INFO @ Sat, 11 Dec 2021 14:22:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:22:52: #2 number of paired peaks: 2305 INFO @ Sat, 11 Dec 2021 14:22:52: start model_add_line... INFO @ Sat, 11 Dec 2021 14:22:52: start X-correlation... INFO @ Sat, 11 Dec 2021 14:22:52: end of X-cor INFO @ Sat, 11 Dec 2021 14:22:52: #2 finished! INFO @ Sat, 11 Dec 2021 14:22:52: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 14:22:52: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 14:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.05_model.r WARNING @ Sat, 11 Dec 2021 14:22:52: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:22:52: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 14:22:52: #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 14:22:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:22:52: 15000000 INFO @ Sat, 11 Dec 2021 14:22:52: 20000000 INFO @ Sat, 11 Dec 2021 14:22:58: 16000000 INFO @ Sat, 11 Dec 2021 14:22:59: 21000000 INFO @ Sat, 11 Dec 2021 14:23:03: 17000000 INFO @ Sat, 11 Dec 2021 14:23:05: 22000000 INFO @ Sat, 11 Dec 2021 14:23:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:23:09: 18000000 INFO @ Sat, 11 Dec 2021 14:23:12: 23000000 INFO @ Sat, 11 Dec 2021 14:23:14: 19000000 INFO @ Sat, 11 Dec 2021 14:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.05_summits.bed INFO @ Sat, 11 Dec 2021 14:23:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11714 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:23:18: 24000000 INFO @ Sat, 11 Dec 2021 14:23:20: 20000000 INFO @ Sat, 11 Dec 2021 14:23:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:23:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:23:21: #1 total tags in treatment: 10262821 INFO @ Sat, 11 Dec 2021 14:23:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:23:21: #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 14:23:22: #1 tags after filtering in treatment: 7441080 INFO @ Sat, 11 Dec 2021 14:23:22: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 11 Dec 2021 14:23:22: #1 finished! INFO @ Sat, 11 Dec 2021 14:23:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:23:22: #2 number of paired peaks: 2305 INFO @ Sat, 11 Dec 2021 14:23:22: start model_add_line... INFO @ Sat, 11 Dec 2021 14:23:22: start X-correlation... INFO @ Sat, 11 Dec 2021 14:23:22: end of X-cor INFO @ Sat, 11 Dec 2021 14:23:22: #2 finished! INFO @ Sat, 11 Dec 2021 14:23:22: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 14:23:22: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 14:23:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.10_model.r WARNING @ Sat, 11 Dec 2021 14:23:22: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:23:22: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 14:23:22: #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 14:23:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:23:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:23:26: 21000000 INFO @ Sat, 11 Dec 2021 14:23:32: 22000000 INFO @ Sat, 11 Dec 2021 14:23:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:23:38: 23000000 INFO @ Sat, 11 Dec 2021 14:23:44: 24000000 INFO @ Sat, 11 Dec 2021 14:23:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:23:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:23:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.10_summits.bed INFO @ Sat, 11 Dec 2021 14:23:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6292 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:23:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:23:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:23:47: #1 total tags in treatment: 10262821 INFO @ Sat, 11 Dec 2021 14:23:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:23:47: #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 14:23:47: #1 tags after filtering in treatment: 7441080 INFO @ Sat, 11 Dec 2021 14:23:47: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 11 Dec 2021 14:23:47: #1 finished! INFO @ Sat, 11 Dec 2021 14:23:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:23:48: #2 number of paired peaks: 2305 INFO @ Sat, 11 Dec 2021 14:23:48: start model_add_line... INFO @ Sat, 11 Dec 2021 14:23:48: start X-correlation... INFO @ Sat, 11 Dec 2021 14:23:48: end of X-cor INFO @ Sat, 11 Dec 2021 14:23:48: #2 finished! INFO @ Sat, 11 Dec 2021 14:23:48: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 14:23:48: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 14:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.20_model.r WARNING @ Sat, 11 Dec 2021 14:23:48: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:23:48: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 14:23:48: #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 14:23:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:24:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:24:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103803/SRX9103803.20_summits.bed INFO @ Sat, 11 Dec 2021 14:24:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1422 records, 4 fields): 3 millis CompletedMACS2peakCalling