Job ID = 12266644 SRX = SRX7806718 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16516348 spots for SRR11186384/SRR11186384.sra Written 16516348 spots for SRR11186384/SRR11186384.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267111 ("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: 00:33:00 16516348 reads; of these: 16516348 (100.00%) were paired; of these: 8846952 (53.56%) aligned concordantly 0 times 5168306 (31.29%) aligned concordantly exactly 1 time 2501090 (15.14%) aligned concordantly >1 times ---- 8846952 pairs aligned concordantly 0 times; of these: 1261498 (14.26%) aligned discordantly 1 time ---- 7585454 pairs aligned 0 times concordantly or discordantly; of these: 15170908 mates make up the pairs; of these: 13538831 (89.24%) aligned 0 times 700261 (4.62%) aligned exactly 1 time 931816 (6.14%) aligned >1 times 59.01% overall alignment rate Time searching: 00:33:00 Overall time: 00:33:00 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 8 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] 1346185 / 8875517 = 0.1517 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 09:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.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 09:46:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:46:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:46:18: 1000000 INFO @ Sat, 03 Apr 2021 09:46:26: 2000000 INFO @ Sat, 03 Apr 2021 09:46:34: 3000000 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 09:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.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 09:46:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:46:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:46:43: 4000000 INFO @ Sat, 03 Apr 2021 09:46:49: 1000000 INFO @ Sat, 03 Apr 2021 09:46:52: 5000000 INFO @ Sat, 03 Apr 2021 09:47:00: 2000000 INFO @ Sat, 03 Apr 2021 09:47:03: 6000000 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 09:47:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.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 09:47:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:47:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:47:10: 3000000 INFO @ Sat, 03 Apr 2021 09:47:16: 7000000 INFO @ Sat, 03 Apr 2021 09:47:22: 4000000 INFO @ Sat, 03 Apr 2021 09:47:23: 1000000 INFO @ Sat, 03 Apr 2021 09:47:26: 8000000 INFO @ Sat, 03 Apr 2021 09:47:34: 5000000 INFO @ Sat, 03 Apr 2021 09:47:36: 9000000 INFO @ Sat, 03 Apr 2021 09:47:39: 2000000 INFO @ Sat, 03 Apr 2021 09:47:45: 6000000 INFO @ Sat, 03 Apr 2021 09:47:46: 10000000 INFO @ Sat, 03 Apr 2021 09:47:52: 3000000 INFO @ Sat, 03 Apr 2021 09:47:56: 11000000 INFO @ Sat, 03 Apr 2021 09:47:56: 7000000 INFO @ Sat, 03 Apr 2021 09:48:03: 4000000 INFO @ Sat, 03 Apr 2021 09:48:05: 12000000 INFO @ Sat, 03 Apr 2021 09:48:06: 8000000 INFO @ Sat, 03 Apr 2021 09:48:15: 13000000 INFO @ Sat, 03 Apr 2021 09:48:15: 9000000 INFO @ Sat, 03 Apr 2021 09:48:18: 5000000 INFO @ Sat, 03 Apr 2021 09:48:25: 14000000 INFO @ Sat, 03 Apr 2021 09:48:27: 10000000 INFO @ Sat, 03 Apr 2021 09:48:29: 6000000 INFO @ Sat, 03 Apr 2021 09:48:38: 11000000 INFO @ Sat, 03 Apr 2021 09:48:39: 15000000 INFO @ Sat, 03 Apr 2021 09:48:39: 7000000 INFO @ Sat, 03 Apr 2021 09:48:49: 12000000 INFO @ Sat, 03 Apr 2021 09:48:50: 16000000 INFO @ Sat, 03 Apr 2021 09:48:50: 8000000 INFO @ Sat, 03 Apr 2021 09:48:59: 13000000 INFO @ Sat, 03 Apr 2021 09:49:00: 9000000 INFO @ Sat, 03 Apr 2021 09:49:00: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:49:00: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:49:00: #1 total tags in treatment: 6405979 INFO @ Sat, 03 Apr 2021 09:49:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:49:00: #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 09:49:00: #1 tags after filtering in treatment: 5403202 INFO @ Sat, 03 Apr 2021 09:49:00: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 09:49:00: #1 finished! INFO @ Sat, 03 Apr 2021 09:49:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:49:01: #2 number of paired peaks: 638 WARNING @ Sat, 03 Apr 2021 09:49:01: Fewer paired peaks (638) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 638 pairs to build model! INFO @ Sat, 03 Apr 2021 09:49:01: start model_add_line... INFO @ Sat, 03 Apr 2021 09:49:01: start X-correlation... INFO @ Sat, 03 Apr 2021 09:49:01: end of X-cor INFO @ Sat, 03 Apr 2021 09:49:01: #2 finished! INFO @ Sat, 03 Apr 2021 09:49:01: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Apr 2021 09:49:01: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 03 Apr 2021 09:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.05_model.r WARNING @ Sat, 03 Apr 2021 09:49:01: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:49:01: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Sat, 03 Apr 2021 09:49:01: #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 09:49:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:49:10: 14000000 INFO @ Sat, 03 Apr 2021 09:49:11: 10000000 INFO @ Sat, 03 Apr 2021 09:49:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:49:19: 15000000 INFO @ Sat, 03 Apr 2021 09:49:21: 11000000 INFO @ Sat, 03 Apr 2021 09:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.05_summits.bed INFO @ Sat, 03 Apr 2021 09:49:25: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (4375 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:49:29: 16000000 INFO @ Sat, 03 Apr 2021 09:49:31: 12000000 INFO @ Sat, 03 Apr 2021 09:49:38: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:49:38: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:49:38: #1 total tags in treatment: 6405979 INFO @ Sat, 03 Apr 2021 09:49:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:49:38: #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 09:49:38: #1 tags after filtering in treatment: 5403202 INFO @ Sat, 03 Apr 2021 09:49:38: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 09:49:38: #1 finished! INFO @ Sat, 03 Apr 2021 09:49:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:49:38: #2 number of paired peaks: 638 WARNING @ Sat, 03 Apr 2021 09:49:38: Fewer paired peaks (638) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 638 pairs to build model! INFO @ Sat, 03 Apr 2021 09:49:38: start model_add_line... INFO @ Sat, 03 Apr 2021 09:49:38: start X-correlation... INFO @ Sat, 03 Apr 2021 09:49:39: end of X-cor INFO @ Sat, 03 Apr 2021 09:49:39: #2 finished! INFO @ Sat, 03 Apr 2021 09:49:39: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Apr 2021 09:49:39: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 03 Apr 2021 09:49:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.10_model.r WARNING @ Sat, 03 Apr 2021 09:49:39: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:49:39: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Sat, 03 Apr 2021 09:49:39: #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 09:49:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:49:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:49:41: 13000000 INFO @ Sat, 03 Apr 2021 09:49:52: 14000000 INFO @ Sat, 03 Apr 2021 09:49:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:50:01: 15000000 INFO @ Sat, 03 Apr 2021 09:50:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:50:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:50:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.10_summits.bed INFO @ Sat, 03 Apr 2021 09:50:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1688 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:50:11: 16000000 INFO @ Sat, 03 Apr 2021 09:50:20: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:50:20: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:50:20: #1 total tags in treatment: 6405979 INFO @ Sat, 03 Apr 2021 09:50:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:50:20: #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 09:50:20: #1 tags after filtering in treatment: 5403202 INFO @ Sat, 03 Apr 2021 09:50:20: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 09:50:20: #1 finished! INFO @ Sat, 03 Apr 2021 09:50:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:50:21: #2 number of paired peaks: 638 WARNING @ Sat, 03 Apr 2021 09:50:21: Fewer paired peaks (638) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 638 pairs to build model! INFO @ Sat, 03 Apr 2021 09:50:21: start model_add_line... INFO @ Sat, 03 Apr 2021 09:50:21: start X-correlation... INFO @ Sat, 03 Apr 2021 09:50:21: end of X-cor INFO @ Sat, 03 Apr 2021 09:50:21: #2 finished! INFO @ Sat, 03 Apr 2021 09:50:21: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Apr 2021 09:50:21: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 03 Apr 2021 09:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.20_model.r WARNING @ Sat, 03 Apr 2021 09:50:21: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:50:21: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Sat, 03 Apr 2021 09:50:21: #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 09:50:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:50:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806718/SRX7806718.20_summits.bed INFO @ Sat, 03 Apr 2021 09:50:47: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (436 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。