Job ID = 14167064 SRX = SRX9343232 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19184162 spots for SRR12877208/SRR12877208.sra Written 19184162 spots for SRR12877208/SRR12877208.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167507 ("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: 00:22:14 19184162 reads; of these: 19184162 (100.00%) were paired; of these: 6448869 (33.62%) aligned concordantly 0 times 10766534 (56.12%) aligned concordantly exactly 1 time 1968759 (10.26%) aligned concordantly >1 times ---- 6448869 pairs aligned concordantly 0 times; of these: 1746139 (27.08%) aligned discordantly 1 time ---- 4702730 pairs aligned 0 times concordantly or discordantly; of these: 9405460 mates make up the pairs; of these: 8321570 (88.48%) aligned 0 times 494343 (5.26%) aligned exactly 1 time 589547 (6.27%) aligned >1 times 78.31% overall alignment rate Time searching: 00:22:14 Overall time: 00:22:14 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] 994671 / 14385605 = 0.0691 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 10:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.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 10:00:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:00:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:01:02: 1000000 INFO @ Fri, 10 Dec 2021 10:01:09: 2000000 INFO @ Fri, 10 Dec 2021 10:01:16: 3000000 INFO @ Fri, 10 Dec 2021 10:01:22: 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 @ Fri, 10 Dec 2021 10:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.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 10:01:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:01:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:01:29: 5000000 INFO @ Fri, 10 Dec 2021 10:01:32: 1000000 INFO @ Fri, 10 Dec 2021 10:01:37: 6000000 INFO @ Fri, 10 Dec 2021 10:01:39: 2000000 INFO @ Fri, 10 Dec 2021 10:01:44: 7000000 INFO @ Fri, 10 Dec 2021 10:01:45: 3000000 INFO @ Fri, 10 Dec 2021 10:01:51: 4000000 INFO @ Fri, 10 Dec 2021 10:01:52: 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 @ Fri, 10 Dec 2021 10:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.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 10:01:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:01:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:01:57: 5000000 INFO @ Fri, 10 Dec 2021 10:01:59: 9000000 INFO @ Fri, 10 Dec 2021 10:02:03: 1000000 INFO @ Fri, 10 Dec 2021 10:02:03: 6000000 INFO @ Fri, 10 Dec 2021 10:02:07: 10000000 INFO @ Fri, 10 Dec 2021 10:02:10: 7000000 INFO @ Fri, 10 Dec 2021 10:02:10: 2000000 INFO @ Fri, 10 Dec 2021 10:02:14: 11000000 INFO @ Fri, 10 Dec 2021 10:02:16: 8000000 INFO @ Fri, 10 Dec 2021 10:02:18: 3000000 INFO @ Fri, 10 Dec 2021 10:02:22: 12000000 INFO @ Fri, 10 Dec 2021 10:02:22: 9000000 INFO @ Fri, 10 Dec 2021 10:02:25: 4000000 INFO @ Fri, 10 Dec 2021 10:02:28: 10000000 INFO @ Fri, 10 Dec 2021 10:02:29: 13000000 INFO @ Fri, 10 Dec 2021 10:02:32: 5000000 INFO @ Fri, 10 Dec 2021 10:02:34: 11000000 INFO @ Fri, 10 Dec 2021 10:02:36: 14000000 INFO @ Fri, 10 Dec 2021 10:02:40: 6000000 INFO @ Fri, 10 Dec 2021 10:02:41: 12000000 INFO @ Fri, 10 Dec 2021 10:02:44: 15000000 INFO @ Fri, 10 Dec 2021 10:02:47: 13000000 INFO @ Fri, 10 Dec 2021 10:02:47: 7000000 INFO @ Fri, 10 Dec 2021 10:02:51: 16000000 INFO @ Fri, 10 Dec 2021 10:02:53: 14000000 INFO @ Fri, 10 Dec 2021 10:02:55: 8000000 INFO @ Fri, 10 Dec 2021 10:02:59: 17000000 INFO @ Fri, 10 Dec 2021 10:02:59: 15000000 INFO @ Fri, 10 Dec 2021 10:03:02: 9000000 INFO @ Fri, 10 Dec 2021 10:03:05: 16000000 INFO @ Fri, 10 Dec 2021 10:03:06: 18000000 INFO @ Fri, 10 Dec 2021 10:03:09: 10000000 INFO @ Fri, 10 Dec 2021 10:03:11: 17000000 INFO @ Fri, 10 Dec 2021 10:03:13: 19000000 INFO @ Fri, 10 Dec 2021 10:03:17: 11000000 INFO @ Fri, 10 Dec 2021 10:03:18: 18000000 INFO @ Fri, 10 Dec 2021 10:03:21: 20000000 INFO @ Fri, 10 Dec 2021 10:03:24: 19000000 INFO @ Fri, 10 Dec 2021 10:03:24: 12000000 INFO @ Fri, 10 Dec 2021 10:03:28: 21000000 INFO @ Fri, 10 Dec 2021 10:03:30: 20000000 INFO @ Fri, 10 Dec 2021 10:03:32: 13000000 INFO @ Fri, 10 Dec 2021 10:03:36: 22000000 INFO @ Fri, 10 Dec 2021 10:03:36: 21000000 INFO @ Fri, 10 Dec 2021 10:03:39: 14000000 INFO @ Fri, 10 Dec 2021 10:03:42: 22000000 INFO @ Fri, 10 Dec 2021 10:03:43: 23000000 INFO @ Fri, 10 Dec 2021 10:03:46: 15000000 INFO @ Fri, 10 Dec 2021 10:03:49: 23000000 INFO @ Fri, 10 Dec 2021 10:03:50: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:03:54: 16000000 INFO @ Fri, 10 Dec 2021 10:03:55: 24000000 INFO @ Fri, 10 Dec 2021 10:03:58: 25000000 INFO @ Fri, 10 Dec 2021 10:04:01: 25000000 INFO @ Fri, 10 Dec 2021 10:04:01: 17000000 INFO @ Fri, 10 Dec 2021 10:04:05: 26000000 INFO @ Fri, 10 Dec 2021 10:04:07: 26000000 INFO @ Fri, 10 Dec 2021 10:04:08: 18000000 INFO @ Fri, 10 Dec 2021 10:04:12: 27000000 INFO @ Fri, 10 Dec 2021 10:04:14: 27000000 INFO @ Fri, 10 Dec 2021 10:04:16: 19000000 INFO @ Fri, 10 Dec 2021 10:04:20: 28000000 INFO @ Fri, 10 Dec 2021 10:04:20: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:04:20: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:04:20: #1 total tags in treatment: 11828013 INFO @ Fri, 10 Dec 2021 10:04:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:04:20: #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 10:04:20: #1 tags after filtering in treatment: 9532275 INFO @ Fri, 10 Dec 2021 10:04:20: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 10:04:20: #1 finished! INFO @ Fri, 10 Dec 2021 10:04:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:04:21: 28000000 INFO @ Fri, 10 Dec 2021 10:04:21: #2 number of paired peaks: 927 WARNING @ Fri, 10 Dec 2021 10:04:21: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Fri, 10 Dec 2021 10:04:21: start model_add_line... INFO @ Fri, 10 Dec 2021 10:04:21: start X-correlation... INFO @ Fri, 10 Dec 2021 10:04:21: end of X-cor INFO @ Fri, 10 Dec 2021 10:04:21: #2 finished! INFO @ Fri, 10 Dec 2021 10:04:21: #2 predicted fragment length is 89 bps INFO @ Fri, 10 Dec 2021 10:04:21: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 10 Dec 2021 10:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.05_model.r WARNING @ Fri, 10 Dec 2021 10:04:21: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:04:21: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Fri, 10 Dec 2021 10:04:21: #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 10:04:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:04:21: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:04:21: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:04:21: #1 total tags in treatment: 11828013 INFO @ Fri, 10 Dec 2021 10:04:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:04:21: #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 10:04:21: #1 tags after filtering in treatment: 9532275 INFO @ Fri, 10 Dec 2021 10:04:21: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 10:04:21: #1 finished! INFO @ Fri, 10 Dec 2021 10:04:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:04:22: #2 number of paired peaks: 927 WARNING @ Fri, 10 Dec 2021 10:04:22: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Fri, 10 Dec 2021 10:04:22: start model_add_line... INFO @ Fri, 10 Dec 2021 10:04:22: start X-correlation... INFO @ Fri, 10 Dec 2021 10:04:22: end of X-cor INFO @ Fri, 10 Dec 2021 10:04:22: #2 finished! INFO @ Fri, 10 Dec 2021 10:04:22: #2 predicted fragment length is 89 bps INFO @ Fri, 10 Dec 2021 10:04:22: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 10 Dec 2021 10:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.10_model.r WARNING @ Fri, 10 Dec 2021 10:04:22: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:04:22: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Fri, 10 Dec 2021 10:04:22: #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 10:04:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:04:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:04:23: 20000000 INFO @ Fri, 10 Dec 2021 10:04:30: 21000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:04:37: 22000000 INFO @ Fri, 10 Dec 2021 10:04:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:04:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:04:44: 23000000 INFO @ Fri, 10 Dec 2021 10:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.05_summits.bed INFO @ Fri, 10 Dec 2021 10:04:50: Done! INFO @ Fri, 10 Dec 2021 10:04:50: 24000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11381 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:04:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:04:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:04:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.10_summits.bed INFO @ Fri, 10 Dec 2021 10:04:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5065 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:04:57: 25000000 INFO @ Fri, 10 Dec 2021 10:05:04: 26000000 INFO @ Fri, 10 Dec 2021 10:05:10: 27000000 INFO @ Fri, 10 Dec 2021 10:05:17: 28000000 INFO @ Fri, 10 Dec 2021 10:05:17: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:05:17: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:05:17: #1 total tags in treatment: 11828013 INFO @ Fri, 10 Dec 2021 10:05:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:05:17: #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 10:05:18: #1 tags after filtering in treatment: 9532275 INFO @ Fri, 10 Dec 2021 10:05:18: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 10:05:18: #1 finished! INFO @ Fri, 10 Dec 2021 10:05:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:05:18: #2 number of paired peaks: 927 WARNING @ Fri, 10 Dec 2021 10:05:18: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Fri, 10 Dec 2021 10:05:18: start model_add_line... INFO @ Fri, 10 Dec 2021 10:05:18: start X-correlation... INFO @ Fri, 10 Dec 2021 10:05:18: end of X-cor INFO @ Fri, 10 Dec 2021 10:05:18: #2 finished! INFO @ Fri, 10 Dec 2021 10:05:18: #2 predicted fragment length is 89 bps INFO @ Fri, 10 Dec 2021 10:05:18: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 10 Dec 2021 10:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.20_model.r WARNING @ Fri, 10 Dec 2021 10:05:18: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:05:18: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Fri, 10 Dec 2021 10:05:18: #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 10:05:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:05:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:05:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:05:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:05:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9343232/SRX9343232.20_summits.bed INFO @ Fri, 10 Dec 2021 10:05:46: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (742 records, 4 fields): 2 millis CompletedMACS2peakCalling