Job ID = 14170103 SRX = SRX8556255 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30287977 spots for SRR12024629/SRR12024629.sra Written 30287977 spots for SRR12024629/SRR12024629.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170755 ("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: 01:03:49 30287977 reads; of these: 30287977 (100.00%) were paired; of these: 22023692 (72.71%) aligned concordantly 0 times 6731360 (22.22%) aligned concordantly exactly 1 time 1532925 (5.06%) aligned concordantly >1 times ---- 22023692 pairs aligned concordantly 0 times; of these: 2003008 (9.09%) aligned discordantly 1 time ---- 20020684 pairs aligned 0 times concordantly or discordantly; of these: 40041368 mates make up the pairs; of these: 38339105 (95.75%) aligned 0 times 581902 (1.45%) aligned exactly 1 time 1120361 (2.80%) aligned >1 times 36.71% overall alignment rate Time searching: 01:03:49 Overall time: 01:03:49 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 20 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] 950213 / 10209149 = 0.0931 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 06:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.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 06:39:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:02: 1000000 INFO @ Sat, 11 Dec 2021 06:40:13: 2000000 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 06:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.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 06:40:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:24: 3000000 INFO @ Sat, 11 Dec 2021 06:40:33: 1000000 INFO @ Sat, 11 Dec 2021 06:40:37: 4000000 INFO @ Sat, 11 Dec 2021 06:40:47: 2000000 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 06:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.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 06:40:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:53: 5000000 INFO @ Sat, 11 Dec 2021 06:41:00: 3000000 INFO @ Sat, 11 Dec 2021 06:41:04: 1000000 INFO @ Sat, 11 Dec 2021 06:41:05: 6000000 INFO @ Sat, 11 Dec 2021 06:41:12: 4000000 INFO @ Sat, 11 Dec 2021 06:41:18: 2000000 INFO @ Sat, 11 Dec 2021 06:41:20: 7000000 INFO @ Sat, 11 Dec 2021 06:41:27: 5000000 INFO @ Sat, 11 Dec 2021 06:41:30: 3000000 INFO @ Sat, 11 Dec 2021 06:41:33: 8000000 INFO @ Sat, 11 Dec 2021 06:41:40: 6000000 INFO @ Sat, 11 Dec 2021 06:41:43: 4000000 INFO @ Sat, 11 Dec 2021 06:41:45: 9000000 INFO @ Sat, 11 Dec 2021 06:41:54: 7000000 INFO @ Sat, 11 Dec 2021 06:41:56: 5000000 INFO @ Sat, 11 Dec 2021 06:41:58: 10000000 INFO @ Sat, 11 Dec 2021 06:42:09: 8000000 INFO @ Sat, 11 Dec 2021 06:42:09: 6000000 INFO @ Sat, 11 Dec 2021 06:42:11: 11000000 INFO @ Sat, 11 Dec 2021 06:42:22: 7000000 INFO @ Sat, 11 Dec 2021 06:42:22: 9000000 INFO @ Sat, 11 Dec 2021 06:42:24: 12000000 INFO @ Sat, 11 Dec 2021 06:42:35: 10000000 INFO @ Sat, 11 Dec 2021 06:42:35: 8000000 INFO @ Sat, 11 Dec 2021 06:42:38: 13000000 INFO @ Sat, 11 Dec 2021 06:42:47: 11000000 INFO @ Sat, 11 Dec 2021 06:42:50: 9000000 INFO @ Sat, 11 Dec 2021 06:42:51: 14000000 INFO @ Sat, 11 Dec 2021 06:43:01: 12000000 INFO @ Sat, 11 Dec 2021 06:43:02: 10000000 INFO @ Sat, 11 Dec 2021 06:43:04: 15000000 INFO @ Sat, 11 Dec 2021 06:43:15: 11000000 INFO @ Sat, 11 Dec 2021 06:43:17: 13000000 INFO @ Sat, 11 Dec 2021 06:43:18: 16000000 INFO @ Sat, 11 Dec 2021 06:43:28: 12000000 INFO @ Sat, 11 Dec 2021 06:43:30: 14000000 INFO @ Sat, 11 Dec 2021 06:43:33: 17000000 INFO @ Sat, 11 Dec 2021 06:43:43: 15000000 INFO @ Sat, 11 Dec 2021 06:43:49: 13000000 INFO @ Sat, 11 Dec 2021 06:43:49: 18000000 INFO @ Sat, 11 Dec 2021 06:43:58: 16000000 INFO @ Sat, 11 Dec 2021 06:44:07: 19000000 INFO @ Sat, 11 Dec 2021 06:44:11: 14000000 INFO @ Sat, 11 Dec 2021 06:44:12: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:44:20: 20000000 INFO @ Sat, 11 Dec 2021 06:44:24: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:44:24: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:44:24: #1 total tags in treatment: 7451655 INFO @ Sat, 11 Dec 2021 06:44:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:44:24: #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 06:44:24: #1 tags after filtering in treatment: 6576522 INFO @ Sat, 11 Dec 2021 06:44:24: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:44:24: #1 finished! INFO @ Sat, 11 Dec 2021 06:44:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:44:24: #2 number of paired peaks: 506 WARNING @ Sat, 11 Dec 2021 06:44:24: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Sat, 11 Dec 2021 06:44:24: start model_add_line... INFO @ Sat, 11 Dec 2021 06:44:24: start X-correlation... INFO @ Sat, 11 Dec 2021 06:44:25: end of X-cor INFO @ Sat, 11 Dec 2021 06:44:25: #2 finished! INFO @ Sat, 11 Dec 2021 06:44:25: #2 predicted fragment length is 217 bps INFO @ Sat, 11 Dec 2021 06:44:25: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 11 Dec 2021 06:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.05_model.r WARNING @ Sat, 11 Dec 2021 06:44:25: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:44:25: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 11 Dec 2021 06:44:25: #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 06:44:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:44:25: 18000000 INFO @ Sat, 11 Dec 2021 06:44:25: 15000000 INFO @ Sat, 11 Dec 2021 06:44:36: 19000000 INFO @ Sat, 11 Dec 2021 06:44:37: 16000000 INFO @ Sat, 11 Dec 2021 06:44:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:47: 20000000 INFO @ Sat, 11 Dec 2021 06:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.05_summits.bed INFO @ Sat, 11 Dec 2021 06:44:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4305 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:44:51: 17000000 INFO @ Sat, 11 Dec 2021 06:44:51: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:44:51: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:44:51: #1 total tags in treatment: 7451655 INFO @ Sat, 11 Dec 2021 06:44:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:44:51: #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 06:44:51: #1 tags after filtering in treatment: 6576522 INFO @ Sat, 11 Dec 2021 06:44:51: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:44:51: #1 finished! INFO @ Sat, 11 Dec 2021 06:44:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:44:52: #2 number of paired peaks: 506 WARNING @ Sat, 11 Dec 2021 06:44:52: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Sat, 11 Dec 2021 06:44:52: start model_add_line... INFO @ Sat, 11 Dec 2021 06:44:52: start X-correlation... INFO @ Sat, 11 Dec 2021 06:44:52: end of X-cor INFO @ Sat, 11 Dec 2021 06:44:52: #2 finished! INFO @ Sat, 11 Dec 2021 06:44:52: #2 predicted fragment length is 217 bps INFO @ Sat, 11 Dec 2021 06:44:52: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 11 Dec 2021 06:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.10_model.r WARNING @ Sat, 11 Dec 2021 06:44:52: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:44:52: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 11 Dec 2021 06:44:52: #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 06:44:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:44:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:45:03: 18000000 INFO @ Sat, 11 Dec 2021 06:45:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.10_summits.bed INFO @ Sat, 11 Dec 2021 06:45:16: 19000000 INFO @ Sat, 11 Dec 2021 06:45:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1646 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:45:30: 20000000 INFO @ Sat, 11 Dec 2021 06:45:34: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:45:34: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:45:34: #1 total tags in treatment: 7451655 INFO @ Sat, 11 Dec 2021 06:45:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:45:34: #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 06:45:35: #1 tags after filtering in treatment: 6576522 INFO @ Sat, 11 Dec 2021 06:45:35: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:45:35: #1 finished! INFO @ Sat, 11 Dec 2021 06:45:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:45:35: #2 number of paired peaks: 506 WARNING @ Sat, 11 Dec 2021 06:45:35: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Sat, 11 Dec 2021 06:45:35: start model_add_line... INFO @ Sat, 11 Dec 2021 06:45:35: start X-correlation... INFO @ Sat, 11 Dec 2021 06:45:35: end of X-cor INFO @ Sat, 11 Dec 2021 06:45:35: #2 finished! INFO @ Sat, 11 Dec 2021 06:45:35: #2 predicted fragment length is 217 bps INFO @ Sat, 11 Dec 2021 06:45:35: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 11 Dec 2021 06:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.20_model.r WARNING @ Sat, 11 Dec 2021 06:45:35: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:45:35: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 11 Dec 2021 06:45:35: #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 06:45:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:45:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556255/SRX8556255.20_summits.bed INFO @ Sat, 11 Dec 2021 06:45:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling