Job ID = 14172050 SRX = SRX9103809 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23196958 spots for SRR12621009/SRR12621009.sra Written 23196958 spots for SRR12621009/SRR12621009.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172546 ("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: 00:20:33 23196958 reads; of these: 23196958 (100.00%) were paired; of these: 8875753 (38.26%) aligned concordantly 0 times 8664286 (37.35%) aligned concordantly exactly 1 time 5656919 (24.39%) aligned concordantly >1 times ---- 8875753 pairs aligned concordantly 0 times; of these: 1103830 (12.44%) aligned discordantly 1 time ---- 7771923 pairs aligned 0 times concordantly or discordantly; of these: 15543846 mates make up the pairs; of these: 14448755 (92.95%) aligned 0 times 407365 (2.62%) aligned exactly 1 time 687726 (4.42%) aligned >1 times 68.86% overall alignment rate Time searching: 00:20:33 Overall time: 00:20:33 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] 3853196 / 15292084 = 0.2520 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 14:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.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 14:23:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:23:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:23:05: 1000000 INFO @ Sat, 11 Dec 2021 14:23:11: 2000000 INFO @ Sat, 11 Dec 2021 14:23:16: 3000000 INFO @ Sat, 11 Dec 2021 14:23:22: 4000000 INFO @ Sat, 11 Dec 2021 14:23:28: 5000000 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 14:23:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.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 14:23:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:23:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:23:36: 6000000 INFO @ Sat, 11 Dec 2021 14:23:38: 1000000 INFO @ Sat, 11 Dec 2021 14:23:42: 7000000 INFO @ Sat, 11 Dec 2021 14:23:44: 2000000 INFO @ Sat, 11 Dec 2021 14:23:49: 8000000 INFO @ Sat, 11 Dec 2021 14:23:50: 3000000 INFO @ Sat, 11 Dec 2021 14:23:55: 9000000 INFO @ Sat, 11 Dec 2021 14:23:56: 4000000 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 14:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.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 14:24:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:24:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:24:01: 10000000 INFO @ Sat, 11 Dec 2021 14:24:01: 5000000 INFO @ Sat, 11 Dec 2021 14:24:06: 1000000 INFO @ Sat, 11 Dec 2021 14:24:07: 11000000 INFO @ Sat, 11 Dec 2021 14:24:07: 6000000 INFO @ Sat, 11 Dec 2021 14:24:12: 2000000 INFO @ Sat, 11 Dec 2021 14:24:13: 7000000 INFO @ Sat, 11 Dec 2021 14:24:14: 12000000 INFO @ Sat, 11 Dec 2021 14:24:18: 3000000 INFO @ Sat, 11 Dec 2021 14:24:19: 8000000 INFO @ Sat, 11 Dec 2021 14:24:20: 13000000 INFO @ Sat, 11 Dec 2021 14:24:24: 4000000 INFO @ Sat, 11 Dec 2021 14:24:25: 9000000 INFO @ Sat, 11 Dec 2021 14:24:26: 14000000 INFO @ Sat, 11 Dec 2021 14:24:30: 5000000 INFO @ Sat, 11 Dec 2021 14:24:31: 10000000 INFO @ Sat, 11 Dec 2021 14:24:33: 15000000 INFO @ Sat, 11 Dec 2021 14:24:35: 6000000 INFO @ Sat, 11 Dec 2021 14:24:37: 11000000 INFO @ Sat, 11 Dec 2021 14:24:39: 16000000 INFO @ Sat, 11 Dec 2021 14:24:41: 7000000 INFO @ Sat, 11 Dec 2021 14:24:43: 12000000 INFO @ Sat, 11 Dec 2021 14:24:44: 17000000 INFO @ Sat, 11 Dec 2021 14:24:47: 8000000 INFO @ Sat, 11 Dec 2021 14:24:49: 13000000 INFO @ Sat, 11 Dec 2021 14:24:50: 18000000 INFO @ Sat, 11 Dec 2021 14:24:53: 9000000 INFO @ Sat, 11 Dec 2021 14:24:55: 14000000 INFO @ Sat, 11 Dec 2021 14:24:56: 19000000 INFO @ Sat, 11 Dec 2021 14:24:59: 10000000 INFO @ Sat, 11 Dec 2021 14:25:01: 15000000 INFO @ Sat, 11 Dec 2021 14:25:03: 20000000 INFO @ Sat, 11 Dec 2021 14:25:05: 11000000 INFO @ Sat, 11 Dec 2021 14:25:07: 16000000 INFO @ Sat, 11 Dec 2021 14:25:09: 21000000 INFO @ Sat, 11 Dec 2021 14:25:11: 12000000 INFO @ Sat, 11 Dec 2021 14:25:12: 17000000 INFO @ Sat, 11 Dec 2021 14:25:15: 22000000 INFO @ Sat, 11 Dec 2021 14:25:17: 13000000 INFO @ Sat, 11 Dec 2021 14:25:18: 18000000 INFO @ Sat, 11 Dec 2021 14:25:21: 23000000 INFO @ Sat, 11 Dec 2021 14:25:23: 14000000 INFO @ Sat, 11 Dec 2021 14:25:24: 19000000 INFO @ Sat, 11 Dec 2021 14:25:27: 24000000 INFO @ Sat, 11 Dec 2021 14:25:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:25:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:25:28: #1 total tags in treatment: 10544302 INFO @ Sat, 11 Dec 2021 14:25:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:25:28: #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 14:25:29: #1 tags after filtering in treatment: 8369204 INFO @ Sat, 11 Dec 2021 14:25:29: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:25:29: #1 finished! INFO @ Sat, 11 Dec 2021 14:25:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:25:29: #2 number of paired peaks: 820 WARNING @ Sat, 11 Dec 2021 14:25:29: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Sat, 11 Dec 2021 14:25:29: start model_add_line... INFO @ Sat, 11 Dec 2021 14:25:29: start X-correlation... INFO @ Sat, 11 Dec 2021 14:25:29: end of X-cor INFO @ Sat, 11 Dec 2021 14:25:29: #2 finished! INFO @ Sat, 11 Dec 2021 14:25:29: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 14:25:29: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 14:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.05_model.r WARNING @ Sat, 11 Dec 2021 14:25:29: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:25:29: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 14:25:29: #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 14:25:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:25:29: 15000000 INFO @ Sat, 11 Dec 2021 14:25:30: 20000000 INFO @ Sat, 11 Dec 2021 14:25:35: 16000000 INFO @ Sat, 11 Dec 2021 14:25:36: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:25:41: 17000000 INFO @ Sat, 11 Dec 2021 14:25:42: 22000000 INFO @ Sat, 11 Dec 2021 14:25:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:25:47: 18000000 INFO @ Sat, 11 Dec 2021 14:25:48: 23000000 INFO @ Sat, 11 Dec 2021 14:25:53: 19000000 INFO @ Sat, 11 Dec 2021 14:25:54: 24000000 INFO @ Sat, 11 Dec 2021 14:25:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:25:55: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:25:55: #1 total tags in treatment: 10544302 INFO @ Sat, 11 Dec 2021 14:25:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:25:55: #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 14:25:55: #1 tags after filtering in treatment: 8369204 INFO @ Sat, 11 Dec 2021 14:25:55: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:25:55: #1 finished! INFO @ Sat, 11 Dec 2021 14:25:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:25:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:25:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:25:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.05_summits.bed INFO @ Sat, 11 Dec 2021 14:25:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7665 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:25:56: #2 number of paired peaks: 820 WARNING @ Sat, 11 Dec 2021 14:25:56: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Sat, 11 Dec 2021 14:25:56: start model_add_line... INFO @ Sat, 11 Dec 2021 14:25:56: start X-correlation... INFO @ Sat, 11 Dec 2021 14:25:56: end of X-cor INFO @ Sat, 11 Dec 2021 14:25:56: #2 finished! INFO @ Sat, 11 Dec 2021 14:25:56: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 14:25:56: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 14:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.10_model.r WARNING @ Sat, 11 Dec 2021 14:25:56: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:25:56: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 14:25:56: #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 14:25:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:25:58: 20000000 INFO @ Sat, 11 Dec 2021 14:26:04: 21000000 INFO @ Sat, 11 Dec 2021 14:26:09: 22000000 INFO @ Sat, 11 Dec 2021 14:26:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:26:14: 23000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:26:19: 24000000 INFO @ Sat, 11 Dec 2021 14:26:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:26:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:26:21: #1 total tags in treatment: 10544302 INFO @ Sat, 11 Dec 2021 14:26:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:26:21: #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 14:26:21: #1 tags after filtering in treatment: 8369204 INFO @ Sat, 11 Dec 2021 14:26:21: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:26:21: #1 finished! INFO @ Sat, 11 Dec 2021 14:26:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:26:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:26:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:26:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.10_summits.bed INFO @ Sat, 11 Dec 2021 14:26:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3604 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:26:21: #2 number of paired peaks: 820 WARNING @ Sat, 11 Dec 2021 14:26:21: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Sat, 11 Dec 2021 14:26:21: start model_add_line... INFO @ Sat, 11 Dec 2021 14:26:22: start X-correlation... INFO @ Sat, 11 Dec 2021 14:26:22: end of X-cor INFO @ Sat, 11 Dec 2021 14:26:22: #2 finished! INFO @ Sat, 11 Dec 2021 14:26:22: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 14:26:22: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 14:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.20_model.r WARNING @ Sat, 11 Dec 2021 14:26:22: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:26:22: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 14:26:22: #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 14:26:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:26:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:26:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:26:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:26:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103809/SRX9103809.20_summits.bed INFO @ Sat, 11 Dec 2021 14:26:47: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 2 millis CompletedMACS2peakCalling