Job ID = 14171735 SRX = SRX10386228 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31045828 spots for SRR14009293/SRR14009293.sra Written 31045828 spots for SRR14009293/SRR14009293.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172496 ("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: 01:12:45 31045828 reads; of these: 31045828 (100.00%) were paired; of these: 10166310 (32.75%) aligned concordantly 0 times 7727550 (24.89%) aligned concordantly exactly 1 time 13151968 (42.36%) aligned concordantly >1 times ---- 10166310 pairs aligned concordantly 0 times; of these: 198858 (1.96%) aligned discordantly 1 time ---- 9967452 pairs aligned 0 times concordantly or discordantly; of these: 19934904 mates make up the pairs; of these: 19108541 (95.85%) aligned 0 times 341863 (1.71%) aligned exactly 1 time 484500 (2.43%) aligned >1 times 69.23% overall alignment rate Time searching: 01:12:45 Overall time: 01:12:45 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] 10960922 / 20907872 = 0.5242 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 14:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.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 14:01:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:01:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:01:46: 1000000 INFO @ Sat, 11 Dec 2021 14:01:51: 2000000 INFO @ Sat, 11 Dec 2021 14:01:56: 3000000 INFO @ Sat, 11 Dec 2021 14:02:01: 4000000 INFO @ Sat, 11 Dec 2021 14:02:06: 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 14:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.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 14:02:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:02:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:02:11: 6000000 INFO @ Sat, 11 Dec 2021 14:02:16: 1000000 INFO @ Sat, 11 Dec 2021 14:02:17: 7000000 INFO @ Sat, 11 Dec 2021 14:02:22: 2000000 INFO @ Sat, 11 Dec 2021 14:02:22: 8000000 INFO @ Sat, 11 Dec 2021 14:02:28: 3000000 INFO @ Sat, 11 Dec 2021 14:02:28: 9000000 INFO @ Sat, 11 Dec 2021 14:02:33: 4000000 INFO @ Sat, 11 Dec 2021 14:02:34: 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 14:02:39: 5000000 INFO @ Sat, 11 Dec 2021 14:02:40: 11000000 INFO @ Sat, 11 Dec 2021 14:02:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.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 14:02:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:02:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:02:45: 6000000 INFO @ Sat, 11 Dec 2021 14:02:45: 12000000 INFO @ Sat, 11 Dec 2021 14:02:46: 1000000 INFO @ Sat, 11 Dec 2021 14:02:51: 7000000 INFO @ Sat, 11 Dec 2021 14:02:51: 13000000 INFO @ Sat, 11 Dec 2021 14:02:52: 2000000 INFO @ Sat, 11 Dec 2021 14:02:56: 8000000 INFO @ Sat, 11 Dec 2021 14:02:57: 14000000 INFO @ Sat, 11 Dec 2021 14:02:58: 3000000 INFO @ Sat, 11 Dec 2021 14:03:02: 9000000 INFO @ Sat, 11 Dec 2021 14:03:03: 15000000 INFO @ Sat, 11 Dec 2021 14:03:04: 4000000 INFO @ Sat, 11 Dec 2021 14:03:08: 10000000 INFO @ Sat, 11 Dec 2021 14:03:08: 16000000 INFO @ Sat, 11 Dec 2021 14:03:09: 5000000 INFO @ Sat, 11 Dec 2021 14:03:14: 11000000 INFO @ Sat, 11 Dec 2021 14:03:14: 17000000 INFO @ Sat, 11 Dec 2021 14:03:15: 6000000 INFO @ Sat, 11 Dec 2021 14:03:20: 12000000 INFO @ Sat, 11 Dec 2021 14:03:20: 18000000 INFO @ Sat, 11 Dec 2021 14:03:21: 7000000 INFO @ Sat, 11 Dec 2021 14:03:25: 19000000 INFO @ Sat, 11 Dec 2021 14:03:26: 13000000 INFO @ Sat, 11 Dec 2021 14:03:27: 8000000 INFO @ Sat, 11 Dec 2021 14:03:31: 20000000 INFO @ Sat, 11 Dec 2021 14:03:31: 14000000 INFO @ Sat, 11 Dec 2021 14:03:33: 9000000 INFO @ Sat, 11 Dec 2021 14:03:37: 21000000 INFO @ Sat, 11 Dec 2021 14:03:37: 15000000 INFO @ Sat, 11 Dec 2021 14:03:37: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:03:37: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:03:37: #1 total tags in treatment: 9960660 INFO @ Sat, 11 Dec 2021 14:03:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:03:37: #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 14:03:37: #1 tags after filtering in treatment: 6958412 INFO @ Sat, 11 Dec 2021 14:03:37: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 14:03:37: #1 finished! INFO @ Sat, 11 Dec 2021 14:03:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:03:38: #2 number of paired peaks: 931 WARNING @ Sat, 11 Dec 2021 14:03:38: Fewer paired peaks (931) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 931 pairs to build model! INFO @ Sat, 11 Dec 2021 14:03:38: start model_add_line... INFO @ Sat, 11 Dec 2021 14:03:38: start X-correlation... INFO @ Sat, 11 Dec 2021 14:03:38: end of X-cor INFO @ Sat, 11 Dec 2021 14:03:38: #2 finished! INFO @ Sat, 11 Dec 2021 14:03:38: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 14:03:38: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 14:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.05_model.r WARNING @ Sat, 11 Dec 2021 14:03:38: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:03:38: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 14:03:38: #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 14:03:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:03:38: 10000000 INFO @ Sat, 11 Dec 2021 14:03:43: 16000000 INFO @ Sat, 11 Dec 2021 14:03:44: 11000000 INFO @ Sat, 11 Dec 2021 14:03:49: 17000000 INFO @ Sat, 11 Dec 2021 14:03:50: 12000000 INFO @ Sat, 11 Dec 2021 14:03:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:03:54: 18000000 INFO @ Sat, 11 Dec 2021 14:03:55: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:04:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:04:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:04:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.05_summits.bed INFO @ Sat, 11 Dec 2021 14:04:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2304 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:04:00: 19000000 INFO @ Sat, 11 Dec 2021 14:04:01: 14000000 INFO @ Sat, 11 Dec 2021 14:04:05: 20000000 INFO @ Sat, 11 Dec 2021 14:04:07: 15000000 INFO @ Sat, 11 Dec 2021 14:04:11: 21000000 INFO @ Sat, 11 Dec 2021 14:04:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:04:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:04:11: #1 total tags in treatment: 9960660 INFO @ Sat, 11 Dec 2021 14:04:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:04:11: #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 14:04:12: #1 tags after filtering in treatment: 6958412 INFO @ Sat, 11 Dec 2021 14:04:12: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 14:04:12: #1 finished! INFO @ Sat, 11 Dec 2021 14:04:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:04:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:04:12: #2 number of paired peaks: 931 WARNING @ Sat, 11 Dec 2021 14:04:12: Fewer paired peaks (931) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 931 pairs to build model! INFO @ Sat, 11 Dec 2021 14:04:12: start model_add_line... INFO @ Sat, 11 Dec 2021 14:04:12: start X-correlation... INFO @ Sat, 11 Dec 2021 14:04:12: end of X-cor INFO @ Sat, 11 Dec 2021 14:04:12: #2 finished! INFO @ Sat, 11 Dec 2021 14:04:12: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 14:04:12: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 14:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.10_model.r WARNING @ Sat, 11 Dec 2021 14:04:12: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:04:12: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 14:04:12: #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 14:04:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:04:12: 16000000 INFO @ Sat, 11 Dec 2021 14:04:18: 17000000 INFO @ Sat, 11 Dec 2021 14:04:23: 18000000 INFO @ Sat, 11 Dec 2021 14:04:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:04:28: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:04:34: 20000000 INFO @ Sat, 11 Dec 2021 14:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.10_summits.bed INFO @ Sat, 11 Dec 2021 14:04:34: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1452 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:04:39: 21000000 INFO @ Sat, 11 Dec 2021 14:04:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:04:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:04:39: #1 total tags in treatment: 9960660 INFO @ Sat, 11 Dec 2021 14:04:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:04:39: #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 14:04:39: #1 tags after filtering in treatment: 6958412 INFO @ Sat, 11 Dec 2021 14:04:39: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 14:04:39: #1 finished! INFO @ Sat, 11 Dec 2021 14:04:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:04:40: #2 number of paired peaks: 931 WARNING @ Sat, 11 Dec 2021 14:04:40: Fewer paired peaks (931) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 931 pairs to build model! INFO @ Sat, 11 Dec 2021 14:04:40: start model_add_line... INFO @ Sat, 11 Dec 2021 14:04:40: start X-correlation... INFO @ Sat, 11 Dec 2021 14:04:40: end of X-cor INFO @ Sat, 11 Dec 2021 14:04:40: #2 finished! INFO @ Sat, 11 Dec 2021 14:04:40: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 14:04:40: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 14:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.20_model.r WARNING @ Sat, 11 Dec 2021 14:04:40: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:04:40: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 14:04:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:04:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:04:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386228/SRX10386228.20_summits.bed INFO @ Sat, 11 Dec 2021 14:05:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (964 records, 4 fields): 3 millis CompletedMACS2peakCalling