Job ID = 14171515 SRX = SRX10386200 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23149086 spots for SRR14009265/SRR14009265.sra Written 23149086 spots for SRR14009265/SRR14009265.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172114 ("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: 00:38:00 23149086 reads; of these: 23149086 (100.00%) were paired; of these: 7656479 (33.07%) aligned concordantly 0 times 10178693 (43.97%) aligned concordantly exactly 1 time 5313914 (22.96%) aligned concordantly >1 times ---- 7656479 pairs aligned concordantly 0 times; of these: 372261 (4.86%) aligned discordantly 1 time ---- 7284218 pairs aligned 0 times concordantly or discordantly; of these: 14568436 mates make up the pairs; of these: 13615875 (93.46%) aligned 0 times 520674 (3.57%) aligned exactly 1 time 431887 (2.96%) aligned >1 times 70.59% overall alignment rate Time searching: 00:38:00 Overall time: 00:38:00 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] 3442177 / 15831014 = 0.2174 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 12:41:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.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 12:41:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:41:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:41:48: 1000000 INFO @ Sat, 11 Dec 2021 12:41:54: 2000000 INFO @ Sat, 11 Dec 2021 12:42:00: 3000000 INFO @ Sat, 11 Dec 2021 12:42:06: 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 12:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.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 12:42:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:42:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:42:12: 5000000 INFO @ Sat, 11 Dec 2021 12:42:17: 1000000 INFO @ Sat, 11 Dec 2021 12:42:18: 6000000 INFO @ Sat, 11 Dec 2021 12:42:24: 2000000 INFO @ Sat, 11 Dec 2021 12:42:25: 7000000 INFO @ Sat, 11 Dec 2021 12:42:30: 3000000 INFO @ Sat, 11 Dec 2021 12:42:31: 8000000 INFO @ Sat, 11 Dec 2021 12:42:37: 4000000 INFO @ Sat, 11 Dec 2021 12:42:38: 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 12:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.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 12:42:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:42:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:42:43: 5000000 INFO @ Sat, 11 Dec 2021 12:42:44: 10000000 INFO @ Sat, 11 Dec 2021 12:42:47: 1000000 INFO @ Sat, 11 Dec 2021 12:42:50: 6000000 INFO @ Sat, 11 Dec 2021 12:42:51: 11000000 INFO @ Sat, 11 Dec 2021 12:42:54: 2000000 INFO @ Sat, 11 Dec 2021 12:42:56: 7000000 INFO @ Sat, 11 Dec 2021 12:42:58: 12000000 INFO @ Sat, 11 Dec 2021 12:43:01: 3000000 INFO @ Sat, 11 Dec 2021 12:43:03: 8000000 INFO @ Sat, 11 Dec 2021 12:43:04: 13000000 INFO @ Sat, 11 Dec 2021 12:43:07: 4000000 INFO @ Sat, 11 Dec 2021 12:43:09: 9000000 INFO @ Sat, 11 Dec 2021 12:43:11: 14000000 INFO @ Sat, 11 Dec 2021 12:43:14: 5000000 INFO @ Sat, 11 Dec 2021 12:43:16: 10000000 INFO @ Sat, 11 Dec 2021 12:43:17: 15000000 INFO @ Sat, 11 Dec 2021 12:43:20: 6000000 INFO @ Sat, 11 Dec 2021 12:43:22: 11000000 INFO @ Sat, 11 Dec 2021 12:43:24: 16000000 INFO @ Sat, 11 Dec 2021 12:43:27: 7000000 INFO @ Sat, 11 Dec 2021 12:43:29: 12000000 INFO @ Sat, 11 Dec 2021 12:43:31: 17000000 INFO @ Sat, 11 Dec 2021 12:43:34: 8000000 INFO @ Sat, 11 Dec 2021 12:43:35: 13000000 INFO @ Sat, 11 Dec 2021 12:43:37: 18000000 INFO @ Sat, 11 Dec 2021 12:43:40: 9000000 INFO @ Sat, 11 Dec 2021 12:43:42: 14000000 INFO @ Sat, 11 Dec 2021 12:43:44: 19000000 INFO @ Sat, 11 Dec 2021 12:43:47: 10000000 INFO @ Sat, 11 Dec 2021 12:43:49: 15000000 INFO @ Sat, 11 Dec 2021 12:43:50: 20000000 INFO @ Sat, 11 Dec 2021 12:43:53: 11000000 INFO @ Sat, 11 Dec 2021 12:43:55: 16000000 INFO @ Sat, 11 Dec 2021 12:43:56: 21000000 INFO @ Sat, 11 Dec 2021 12:44:00: 12000000 INFO @ Sat, 11 Dec 2021 12:44:02: 17000000 INFO @ Sat, 11 Dec 2021 12:44:03: 22000000 INFO @ Sat, 11 Dec 2021 12:44:07: 13000000 INFO @ Sat, 11 Dec 2021 12:44:08: 18000000 INFO @ Sat, 11 Dec 2021 12:44:09: 23000000 INFO @ Sat, 11 Dec 2021 12:44:13: 14000000 INFO @ Sat, 11 Dec 2021 12:44:15: 19000000 INFO @ Sat, 11 Dec 2021 12:44:15: 24000000 INFO @ Sat, 11 Dec 2021 12:44:20: 15000000 INFO @ Sat, 11 Dec 2021 12:44:21: 20000000 INFO @ Sat, 11 Dec 2021 12:44:21: 25000000 INFO @ Sat, 11 Dec 2021 12:44:26: 16000000 INFO @ Sat, 11 Dec 2021 12:44:26: #1 tag size is determined as 62 bps INFO @ Sat, 11 Dec 2021 12:44:26: #1 tag size = 62 INFO @ Sat, 11 Dec 2021 12:44:26: #1 total tags in treatment: 12095392 INFO @ Sat, 11 Dec 2021 12:44:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:44:26: #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 12:44:27: #1 tags after filtering in treatment: 10268540 INFO @ Sat, 11 Dec 2021 12:44:27: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 12:44:27: #1 finished! INFO @ Sat, 11 Dec 2021 12:44:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:44:27: 21000000 INFO @ Sat, 11 Dec 2021 12:44:27: #2 number of paired peaks: 272 WARNING @ Sat, 11 Dec 2021 12:44:27: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Sat, 11 Dec 2021 12:44:27: start model_add_line... INFO @ Sat, 11 Dec 2021 12:44:27: start X-correlation... INFO @ Sat, 11 Dec 2021 12:44:27: end of X-cor INFO @ Sat, 11 Dec 2021 12:44:27: #2 finished! INFO @ Sat, 11 Dec 2021 12:44:27: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 12:44:27: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 12:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.05_model.r WARNING @ Sat, 11 Dec 2021 12:44:28: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:44:28: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 11 Dec 2021 12:44:28: #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 12:44:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:44:33: 17000000 INFO @ Sat, 11 Dec 2021 12:44:33: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:44:39: 18000000 INFO @ Sat, 11 Dec 2021 12:44:40: 23000000 INFO @ Sat, 11 Dec 2021 12:44:46: 24000000 INFO @ Sat, 11 Dec 2021 12:44:46: 19000000 INFO @ Sat, 11 Dec 2021 12:44:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:44:52: 25000000 INFO @ Sat, 11 Dec 2021 12:44:52: 20000000 INFO @ Sat, 11 Dec 2021 12:44:57: #1 tag size is determined as 62 bps INFO @ Sat, 11 Dec 2021 12:44:57: #1 tag size = 62 INFO @ Sat, 11 Dec 2021 12:44:57: #1 total tags in treatment: 12095392 INFO @ Sat, 11 Dec 2021 12:44:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:44:57: #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 12:44:57: #1 tags after filtering in treatment: 10268540 INFO @ Sat, 11 Dec 2021 12:44:57: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 12:44:57: #1 finished! INFO @ Sat, 11 Dec 2021 12:44:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:44:58: #2 number of paired peaks: 272 WARNING @ Sat, 11 Dec 2021 12:44:58: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Sat, 11 Dec 2021 12:44:58: start model_add_line... INFO @ Sat, 11 Dec 2021 12:44:58: start X-correlation... INFO @ Sat, 11 Dec 2021 12:44:58: end of X-cor INFO @ Sat, 11 Dec 2021 12:44:58: #2 finished! INFO @ Sat, 11 Dec 2021 12:44:58: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 12:44:58: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 12:44:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.10_model.r WARNING @ Sat, 11 Dec 2021 12:44:58: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:44:58: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 11 Dec 2021 12:44:58: #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 12:44:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.05_summits.bed INFO @ Sat, 11 Dec 2021 12:44:58: Done! INFO @ Sat, 11 Dec 2021 12:44:59: 21000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1770 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:45:05: 22000000 INFO @ Sat, 11 Dec 2021 12:45:11: 23000000 INFO @ Sat, 11 Dec 2021 12:45:17: 24000000 INFO @ Sat, 11 Dec 2021 12:45:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:45:23: 25000000 INFO @ Sat, 11 Dec 2021 12:45:28: #1 tag size is determined as 62 bps INFO @ Sat, 11 Dec 2021 12:45:28: #1 tag size = 62 INFO @ Sat, 11 Dec 2021 12:45:28: #1 total tags in treatment: 12095392 INFO @ Sat, 11 Dec 2021 12:45:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:45:28: #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 12:45:28: #1 tags after filtering in treatment: 10268540 INFO @ Sat, 11 Dec 2021 12:45:28: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 12:45:28: #1 finished! INFO @ Sat, 11 Dec 2021 12:45:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.10_summits.bed INFO @ Sat, 11 Dec 2021 12:45:28: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1092 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:45:29: #2 number of paired peaks: 272 WARNING @ Sat, 11 Dec 2021 12:45:29: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Sat, 11 Dec 2021 12:45:29: start model_add_line... INFO @ Sat, 11 Dec 2021 12:45:29: start X-correlation... INFO @ Sat, 11 Dec 2021 12:45:29: end of X-cor INFO @ Sat, 11 Dec 2021 12:45:29: #2 finished! INFO @ Sat, 11 Dec 2021 12:45:29: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 12:45:29: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 12:45:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.20_model.r WARNING @ Sat, 11 Dec 2021 12:45:29: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:45:29: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 11 Dec 2021 12:45:29: #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 12:45:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:45:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386200/SRX10386200.20_summits.bed INFO @ Sat, 11 Dec 2021 12:45:59: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 4 millis CompletedMACS2peakCalling