Job ID = 14171788 SRX = SRX9008837 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12372658 spots for SRR12518309/SRR12518309.sra Written 12372658 spots for SRR12518309/SRR12518309.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172308 ("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: 00:24:35 12372658 reads; of these: 12372658 (100.00%) were paired; of these: 1969136 (15.92%) aligned concordantly 0 times 8556283 (69.15%) aligned concordantly exactly 1 time 1847239 (14.93%) aligned concordantly >1 times ---- 1969136 pairs aligned concordantly 0 times; of these: 1083687 (55.03%) aligned discordantly 1 time ---- 885449 pairs aligned 0 times concordantly or discordantly; of these: 1770898 mates make up the pairs; of these: 1100565 (62.15%) aligned 0 times 280323 (15.83%) aligned exactly 1 time 390010 (22.02%) aligned >1 times 95.55% overall alignment rate Time searching: 00:24:35 Overall time: 00:24:35 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 12 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] 701818 / 11411892 = 0.0615 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 13:23:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.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 13:23:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:22: 1000000 INFO @ Sat, 11 Dec 2021 13:23:28: 2000000 INFO @ Sat, 11 Dec 2021 13:23:34: 3000000 INFO @ Sat, 11 Dec 2021 13:23:39: 4000000 INFO @ Sat, 11 Dec 2021 13:23:45: 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 13:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.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 13:23:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:51: 6000000 INFO @ Sat, 11 Dec 2021 13:23:53: 1000000 INFO @ Sat, 11 Dec 2021 13:23:57: 7000000 INFO @ Sat, 11 Dec 2021 13:23:59: 2000000 INFO @ Sat, 11 Dec 2021 13:24:03: 8000000 INFO @ Sat, 11 Dec 2021 13:24:05: 3000000 INFO @ Sat, 11 Dec 2021 13:24:09: 9000000 INFO @ Sat, 11 Dec 2021 13:24:11: 4000000 INFO @ Sat, 11 Dec 2021 13:24:15: 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 13:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.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 13:24:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:24:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:24:17: 5000000 INFO @ Sat, 11 Dec 2021 13:24:21: 11000000 INFO @ Sat, 11 Dec 2021 13:24:23: 6000000 INFO @ Sat, 11 Dec 2021 13:24:24: 1000000 INFO @ Sat, 11 Dec 2021 13:24:27: 12000000 INFO @ Sat, 11 Dec 2021 13:24:30: 7000000 INFO @ Sat, 11 Dec 2021 13:24:30: 2000000 INFO @ Sat, 11 Dec 2021 13:24:34: 13000000 INFO @ Sat, 11 Dec 2021 13:24:36: 8000000 INFO @ Sat, 11 Dec 2021 13:24:36: 3000000 INFO @ Sat, 11 Dec 2021 13:24:40: 14000000 INFO @ Sat, 11 Dec 2021 13:24:42: 9000000 INFO @ Sat, 11 Dec 2021 13:24:43: 4000000 INFO @ Sat, 11 Dec 2021 13:24:46: 15000000 INFO @ Sat, 11 Dec 2021 13:24:49: 10000000 INFO @ Sat, 11 Dec 2021 13:24:49: 5000000 INFO @ Sat, 11 Dec 2021 13:24:52: 16000000 INFO @ Sat, 11 Dec 2021 13:24:55: 11000000 INFO @ Sat, 11 Dec 2021 13:24:55: 6000000 INFO @ Sat, 11 Dec 2021 13:24:59: 17000000 INFO @ Sat, 11 Dec 2021 13:25:01: 12000000 INFO @ Sat, 11 Dec 2021 13:25:02: 7000000 INFO @ Sat, 11 Dec 2021 13:25:05: 18000000 INFO @ Sat, 11 Dec 2021 13:25:07: 13000000 INFO @ Sat, 11 Dec 2021 13:25:08: 8000000 INFO @ Sat, 11 Dec 2021 13:25:11: 19000000 INFO @ Sat, 11 Dec 2021 13:25:13: 14000000 INFO @ Sat, 11 Dec 2021 13:25:14: 9000000 INFO @ Sat, 11 Dec 2021 13:25:18: 20000000 INFO @ Sat, 11 Dec 2021 13:25:19: 15000000 INFO @ Sat, 11 Dec 2021 13:25:20: 10000000 INFO @ Sat, 11 Dec 2021 13:25:24: 21000000 INFO @ Sat, 11 Dec 2021 13:25:26: 16000000 INFO @ Sat, 11 Dec 2021 13:25:26: 11000000 INFO @ Sat, 11 Dec 2021 13:25:30: 22000000 INFO @ Sat, 11 Dec 2021 13:25:31: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:25:31: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:25:31: #1 total tags in treatment: 9768459 INFO @ Sat, 11 Dec 2021 13:25:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:25:31: #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 13:25:32: #1 tags after filtering in treatment: 9419685 INFO @ Sat, 11 Dec 2021 13:25:32: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:25:32: #1 finished! INFO @ Sat, 11 Dec 2021 13:25:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:25:32: 17000000 INFO @ Sat, 11 Dec 2021 13:25:32: #2 number of paired peaks: 133 WARNING @ Sat, 11 Dec 2021 13:25:32: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 11 Dec 2021 13:25:32: start model_add_line... INFO @ Sat, 11 Dec 2021 13:25:32: start X-correlation... INFO @ Sat, 11 Dec 2021 13:25:32: end of X-cor INFO @ Sat, 11 Dec 2021 13:25:32: #2 finished! INFO @ Sat, 11 Dec 2021 13:25:32: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 13:25:32: #2 alternative fragment length(s) may be 3,131,158,179,569,590 bps INFO @ Sat, 11 Dec 2021 13:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.05_model.r WARNING @ Sat, 11 Dec 2021 13:25:32: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:25:32: #2 You may need to consider one of the other alternative d(s): 3,131,158,179,569,590 WARNING @ Sat, 11 Dec 2021 13:25:32: #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 13:25:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:25:32: 12000000 INFO @ Sat, 11 Dec 2021 13:25:38: 18000000 INFO @ Sat, 11 Dec 2021 13:25:39: 13000000 INFO @ Sat, 11 Dec 2021 13:25:44: 19000000 INFO @ Sat, 11 Dec 2021 13:25:45: 14000000 INFO @ Sat, 11 Dec 2021 13:25:50: 20000000 INFO @ Sat, 11 Dec 2021 13:25:51: 15000000 INFO @ Sat, 11 Dec 2021 13:25:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:25:57: 21000000 INFO @ Sat, 11 Dec 2021 13:25:57: 16000000 INFO @ Sat, 11 Dec 2021 13:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.05_summits.bed INFO @ Sat, 11 Dec 2021 13:26:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (495 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:26:03: 22000000 INFO @ Sat, 11 Dec 2021 13:26:03: 17000000 INFO @ Sat, 11 Dec 2021 13:26:04: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:26:04: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:26:04: #1 total tags in treatment: 9768459 INFO @ Sat, 11 Dec 2021 13:26:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:26:04: #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 13:26:05: #1 tags after filtering in treatment: 9419685 INFO @ Sat, 11 Dec 2021 13:26:05: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:26:05: #1 finished! INFO @ Sat, 11 Dec 2021 13:26:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:26:05: #2 number of paired peaks: 133 WARNING @ Sat, 11 Dec 2021 13:26:05: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 11 Dec 2021 13:26:05: start model_add_line... INFO @ Sat, 11 Dec 2021 13:26:05: start X-correlation... INFO @ Sat, 11 Dec 2021 13:26:05: end of X-cor INFO @ Sat, 11 Dec 2021 13:26:05: #2 finished! INFO @ Sat, 11 Dec 2021 13:26:05: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 13:26:05: #2 alternative fragment length(s) may be 3,131,158,179,569,590 bps INFO @ Sat, 11 Dec 2021 13:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.10_model.r WARNING @ Sat, 11 Dec 2021 13:26:05: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:26:05: #2 You may need to consider one of the other alternative d(s): 3,131,158,179,569,590 WARNING @ Sat, 11 Dec 2021 13:26:05: #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 13:26:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:26:09: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:26:15: 19000000 INFO @ Sat, 11 Dec 2021 13:26:21: 20000000 INFO @ Sat, 11 Dec 2021 13:26:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:26:27: 21000000 INFO @ Sat, 11 Dec 2021 13:26:33: 22000000 INFO @ Sat, 11 Dec 2021 13:26:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:26:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:26:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.10_summits.bed INFO @ Sat, 11 Dec 2021 13:26:33: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (174 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:26:34: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:26:34: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:26:34: #1 total tags in treatment: 9768459 INFO @ Sat, 11 Dec 2021 13:26:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:26:34: #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 13:26:34: #1 tags after filtering in treatment: 9419685 INFO @ Sat, 11 Dec 2021 13:26:34: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:26:34: #1 finished! INFO @ Sat, 11 Dec 2021 13:26:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:26:35: #2 number of paired peaks: 133 WARNING @ Sat, 11 Dec 2021 13:26:35: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 11 Dec 2021 13:26:35: start model_add_line... INFO @ Sat, 11 Dec 2021 13:26:35: start X-correlation... INFO @ Sat, 11 Dec 2021 13:26:35: end of X-cor INFO @ Sat, 11 Dec 2021 13:26:35: #2 finished! INFO @ Sat, 11 Dec 2021 13:26:35: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 13:26:35: #2 alternative fragment length(s) may be 3,131,158,179,569,590 bps INFO @ Sat, 11 Dec 2021 13:26:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.20_model.r WARNING @ Sat, 11 Dec 2021 13:26:35: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:26:35: #2 You may need to consider one of the other alternative d(s): 3,131,158,179,569,590 WARNING @ Sat, 11 Dec 2021 13:26:35: #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 13:26:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:26:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:26:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008837/SRX9008837.20_summits.bed INFO @ Sat, 11 Dec 2021 13:27:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 1 millis CompletedMACS2peakCalling