Job ID = 12265530 SRX = SRX7277016 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21987200 spots for SRR10597281/SRR10597281.sra Written 21987200 spots for SRR10597281/SRR10597281.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265794 ("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: 00:36:03 21987200 reads; of these: 21987200 (100.00%) were paired; of these: 8865889 (40.32%) aligned concordantly 0 times 9106578 (41.42%) aligned concordantly exactly 1 time 4014733 (18.26%) aligned concordantly >1 times ---- 8865889 pairs aligned concordantly 0 times; of these: 2124877 (23.97%) aligned discordantly 1 time ---- 6741012 pairs aligned 0 times concordantly or discordantly; of these: 13482024 mates make up the pairs; of these: 11029435 (81.81%) aligned 0 times 613344 (4.55%) aligned exactly 1 time 1839245 (13.64%) aligned >1 times 74.92% overall alignment rate Time searching: 00:36:03 Overall time: 00:36:03 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] 2064523 / 15133474 = 0.1364 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.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, 03 Apr 2021 08:21:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:21:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:21:54: 1000000 INFO @ Sat, 03 Apr 2021 08:22:05: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.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, 03 Apr 2021 08:22:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:16: 3000000 INFO @ Sat, 03 Apr 2021 08:22:22: 1000000 INFO @ Sat, 03 Apr 2021 08:22:27: 4000000 INFO @ Sat, 03 Apr 2021 08:22:30: 2000000 INFO @ Sat, 03 Apr 2021 08:22:38: 5000000 INFO @ Sat, 03 Apr 2021 08:22:39: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:22:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.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, 03 Apr 2021 08:22:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:47: 4000000 INFO @ Sat, 03 Apr 2021 08:22:50: 6000000 INFO @ Sat, 03 Apr 2021 08:22:52: 1000000 INFO @ Sat, 03 Apr 2021 08:22:57: 5000000 INFO @ Sat, 03 Apr 2021 08:23:01: 7000000 INFO @ Sat, 03 Apr 2021 08:23:02: 2000000 INFO @ Sat, 03 Apr 2021 08:23:06: 6000000 INFO @ Sat, 03 Apr 2021 08:23:11: 3000000 INFO @ Sat, 03 Apr 2021 08:23:12: 8000000 INFO @ Sat, 03 Apr 2021 08:23:15: 7000000 INFO @ Sat, 03 Apr 2021 08:23:21: 4000000 INFO @ Sat, 03 Apr 2021 08:23:22: 9000000 INFO @ Sat, 03 Apr 2021 08:23:24: 8000000 INFO @ Sat, 03 Apr 2021 08:23:30: 5000000 INFO @ Sat, 03 Apr 2021 08:23:33: 10000000 INFO @ Sat, 03 Apr 2021 08:23:33: 9000000 INFO @ Sat, 03 Apr 2021 08:23:39: 6000000 INFO @ Sat, 03 Apr 2021 08:23:42: 10000000 INFO @ Sat, 03 Apr 2021 08:23:43: 11000000 INFO @ Sat, 03 Apr 2021 08:23:49: 7000000 INFO @ Sat, 03 Apr 2021 08:23:51: 11000000 INFO @ Sat, 03 Apr 2021 08:23:54: 12000000 INFO @ Sat, 03 Apr 2021 08:23:58: 8000000 INFO @ Sat, 03 Apr 2021 08:24:01: 12000000 INFO @ Sat, 03 Apr 2021 08:24:05: 13000000 INFO @ Sat, 03 Apr 2021 08:24:07: 9000000 INFO @ Sat, 03 Apr 2021 08:24:09: 13000000 INFO @ Sat, 03 Apr 2021 08:24:15: 10000000 INFO @ Sat, 03 Apr 2021 08:24:16: 14000000 INFO @ Sat, 03 Apr 2021 08:24:17: 14000000 INFO @ Sat, 03 Apr 2021 08:24:23: 11000000 INFO @ Sat, 03 Apr 2021 08:24:25: 15000000 INFO @ Sat, 03 Apr 2021 08:24:26: 15000000 INFO @ Sat, 03 Apr 2021 08:24:31: 12000000 INFO @ Sat, 03 Apr 2021 08:24:33: 16000000 INFO @ Sat, 03 Apr 2021 08:24:37: 16000000 INFO @ Sat, 03 Apr 2021 08:24:39: 13000000 INFO @ Sat, 03 Apr 2021 08:24:41: 17000000 INFO @ Sat, 03 Apr 2021 08:24:47: 14000000 INFO @ Sat, 03 Apr 2021 08:24:48: 17000000 INFO @ Sat, 03 Apr 2021 08:24:49: 18000000 INFO @ Sat, 03 Apr 2021 08:24:55: 15000000 INFO @ Sat, 03 Apr 2021 08:24:58: 19000000 INFO @ Sat, 03 Apr 2021 08:24:59: 18000000 INFO @ Sat, 03 Apr 2021 08:25:03: 16000000 INFO @ Sat, 03 Apr 2021 08:25:06: 20000000 INFO @ Sat, 03 Apr 2021 08:25:10: 19000000 INFO @ Sat, 03 Apr 2021 08:25:11: 17000000 INFO @ Sat, 03 Apr 2021 08:25:13: 21000000 INFO @ Sat, 03 Apr 2021 08:25:19: 18000000 INFO @ Sat, 03 Apr 2021 08:25:20: 20000000 INFO @ Sat, 03 Apr 2021 08:25:21: 22000000 INFO @ Sat, 03 Apr 2021 08:25:27: 19000000 INFO @ Sat, 03 Apr 2021 08:25:29: 23000000 INFO @ Sat, 03 Apr 2021 08:25:30: 21000000 INFO @ Sat, 03 Apr 2021 08:25:35: 20000000 INFO @ Sat, 03 Apr 2021 08:25:37: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:25:40: 22000000 INFO @ Sat, 03 Apr 2021 08:25:43: 21000000 INFO @ Sat, 03 Apr 2021 08:25:45: 25000000 INFO @ Sat, 03 Apr 2021 08:25:50: 23000000 INFO @ Sat, 03 Apr 2021 08:25:51: 22000000 INFO @ Sat, 03 Apr 2021 08:25:53: 26000000 INFO @ Sat, 03 Apr 2021 08:25:59: 23000000 INFO @ Sat, 03 Apr 2021 08:26:00: 24000000 INFO @ Sat, 03 Apr 2021 08:26:01: 27000000 INFO @ Sat, 03 Apr 2021 08:26:07: 24000000 INFO @ Sat, 03 Apr 2021 08:26:08: 25000000 INFO @ Sat, 03 Apr 2021 08:26:09: 28000000 INFO @ Sat, 03 Apr 2021 08:26:15: 25000000 INFO @ Sat, 03 Apr 2021 08:26:16: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:26:16: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:26:16: #1 total tags in treatment: 11129765 INFO @ Sat, 03 Apr 2021 08:26:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:26:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:26:16: #1 tags after filtering in treatment: 9220947 INFO @ Sat, 03 Apr 2021 08:26:16: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 08:26:16: #1 finished! INFO @ Sat, 03 Apr 2021 08:26:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:26:16: 26000000 INFO @ Sat, 03 Apr 2021 08:26:17: #2 number of paired peaks: 148 WARNING @ Sat, 03 Apr 2021 08:26:17: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 03 Apr 2021 08:26:17: start model_add_line... INFO @ Sat, 03 Apr 2021 08:26:17: start X-correlation... INFO @ Sat, 03 Apr 2021 08:26:17: end of X-cor INFO @ Sat, 03 Apr 2021 08:26:17: #2 finished! INFO @ Sat, 03 Apr 2021 08:26:17: #2 predicted fragment length is 100 bps INFO @ Sat, 03 Apr 2021 08:26:17: #2 alternative fragment length(s) may be 4,100,541,544,581 bps INFO @ Sat, 03 Apr 2021 08:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.10_model.r WARNING @ Sat, 03 Apr 2021 08:26:17: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:26:17: #2 You may need to consider one of the other alternative d(s): 4,100,541,544,581 WARNING @ Sat, 03 Apr 2021 08:26:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:26:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:26:23: 26000000 INFO @ Sat, 03 Apr 2021 08:26:24: 27000000 INFO @ Sat, 03 Apr 2021 08:26:30: 27000000 INFO @ Sat, 03 Apr 2021 08:26:32: 28000000 INFO @ Sat, 03 Apr 2021 08:26:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:26:38: 28000000 INFO @ Sat, 03 Apr 2021 08:26:39: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:26:39: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:26:39: #1 total tags in treatment: 11129765 INFO @ Sat, 03 Apr 2021 08:26:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:26:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:26:39: #1 tags after filtering in treatment: 9220947 INFO @ Sat, 03 Apr 2021 08:26:39: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 08:26:39: #1 finished! INFO @ Sat, 03 Apr 2021 08:26:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:26:40: #2 number of paired peaks: 148 WARNING @ Sat, 03 Apr 2021 08:26:40: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 03 Apr 2021 08:26:40: start model_add_line... INFO @ Sat, 03 Apr 2021 08:26:40: start X-correlation... INFO @ Sat, 03 Apr 2021 08:26:40: end of X-cor INFO @ Sat, 03 Apr 2021 08:26:40: #2 finished! INFO @ Sat, 03 Apr 2021 08:26:40: #2 predicted fragment length is 100 bps INFO @ Sat, 03 Apr 2021 08:26:40: #2 alternative fragment length(s) may be 4,100,541,544,581 bps INFO @ Sat, 03 Apr 2021 08:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.05_model.r WARNING @ Sat, 03 Apr 2021 08:26:40: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:26:40: #2 You may need to consider one of the other alternative d(s): 4,100,541,544,581 WARNING @ Sat, 03 Apr 2021 08:26:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:26:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:26:44: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:26:44: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:26:44: #1 total tags in treatment: 11129765 INFO @ Sat, 03 Apr 2021 08:26:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:26:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:26:44: #1 tags after filtering in treatment: 9220947 INFO @ Sat, 03 Apr 2021 08:26:44: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 08:26:44: #1 finished! INFO @ Sat, 03 Apr 2021 08:26:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:26:44: #2 number of paired peaks: 148 WARNING @ Sat, 03 Apr 2021 08:26:44: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 03 Apr 2021 08:26:44: start model_add_line... INFO @ Sat, 03 Apr 2021 08:26:45: start X-correlation... INFO @ Sat, 03 Apr 2021 08:26:45: end of X-cor INFO @ Sat, 03 Apr 2021 08:26:45: #2 finished! INFO @ Sat, 03 Apr 2021 08:26:45: #2 predicted fragment length is 100 bps INFO @ Sat, 03 Apr 2021 08:26:45: #2 alternative fragment length(s) may be 4,100,541,544,581 bps INFO @ Sat, 03 Apr 2021 08:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.20_model.r WARNING @ Sat, 03 Apr 2021 08:26:45: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:26:45: #2 You may need to consider one of the other alternative d(s): 4,100,541,544,581 WARNING @ Sat, 03 Apr 2021 08:26:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:26:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.10_summits.bed INFO @ Sat, 03 Apr 2021 08:26:45: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:26:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:27:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.05_summits.bed INFO @ Sat, 03 Apr 2021 08:27:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4201 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277016/SRX7277016.20_summits.bed INFO @ Sat, 03 Apr 2021 08:27:12: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (121 records, 4 fields): 2 millis CompletedMACS2peakCalling