Job ID = 14170587 SRX = SRX8497045 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13607738 spots for SRR11952644/SRR11952644.sra Written 13607738 spots for SRR11952644/SRR11952644.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171074 ("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: 00:29:18 13607738 reads; of these: 13607738 (100.00%) were paired; of these: 2258553 (16.60%) aligned concordantly 0 times 8477814 (62.30%) aligned concordantly exactly 1 time 2871371 (21.10%) aligned concordantly >1 times ---- 2258553 pairs aligned concordantly 0 times; of these: 800790 (35.46%) aligned discordantly 1 time ---- 1457763 pairs aligned 0 times concordantly or discordantly; of these: 2915526 mates make up the pairs; of these: 2111619 (72.43%) aligned 0 times 258084 (8.85%) aligned exactly 1 time 545823 (18.72%) aligned >1 times 92.24% overall alignment rate Time searching: 00:29:18 Overall time: 00:29:18 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] 439507 / 12074962 = 0.0364 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 07:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.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 07:58:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:58:46: 1000000 INFO @ Sat, 11 Dec 2021 07:58:53: 2000000 INFO @ Sat, 11 Dec 2021 07:59:00: 3000000 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 07:59:07: 4000000 INFO @ Sat, 11 Dec 2021 07:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.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 07:59:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:59:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:59:14: 5000000 INFO @ Sat, 11 Dec 2021 07:59:15: 1000000 INFO @ Sat, 11 Dec 2021 07:59:21: 2000000 INFO @ Sat, 11 Dec 2021 07:59:22: 6000000 INFO @ Sat, 11 Dec 2021 07:59:26: 3000000 INFO @ Sat, 11 Dec 2021 07:59:29: 7000000 INFO @ Sat, 11 Dec 2021 07:59:32: 4000000 INFO @ Sat, 11 Dec 2021 07:59:36: 8000000 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 07:59:38: 5000000 INFO @ Sat, 11 Dec 2021 07:59:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.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 07:59:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:59:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:59:44: 9000000 INFO @ Sat, 11 Dec 2021 07:59:44: 6000000 INFO @ Sat, 11 Dec 2021 07:59:46: 1000000 INFO @ Sat, 11 Dec 2021 07:59:50: 7000000 INFO @ Sat, 11 Dec 2021 07:59:51: 10000000 INFO @ Sat, 11 Dec 2021 07:59:53: 2000000 INFO @ Sat, 11 Dec 2021 07:59:56: 8000000 INFO @ Sat, 11 Dec 2021 07:59:59: 11000000 INFO @ Sat, 11 Dec 2021 08:00:01: 3000000 INFO @ Sat, 11 Dec 2021 08:00:03: 9000000 INFO @ Sat, 11 Dec 2021 08:00:06: 12000000 INFO @ Sat, 11 Dec 2021 08:00:08: 4000000 INFO @ Sat, 11 Dec 2021 08:00:09: 10000000 INFO @ Sat, 11 Dec 2021 08:00:13: 13000000 INFO @ Sat, 11 Dec 2021 08:00:15: 11000000 INFO @ Sat, 11 Dec 2021 08:00:16: 5000000 INFO @ Sat, 11 Dec 2021 08:00:21: 14000000 INFO @ Sat, 11 Dec 2021 08:00:21: 12000000 INFO @ Sat, 11 Dec 2021 08:00:23: 6000000 INFO @ Sat, 11 Dec 2021 08:00:27: 13000000 INFO @ Sat, 11 Dec 2021 08:00:28: 15000000 INFO @ Sat, 11 Dec 2021 08:00:30: 7000000 INFO @ Sat, 11 Dec 2021 08:00:33: 14000000 INFO @ Sat, 11 Dec 2021 08:00:35: 16000000 INFO @ Sat, 11 Dec 2021 08:00:38: 8000000 INFO @ Sat, 11 Dec 2021 08:00:39: 15000000 INFO @ Sat, 11 Dec 2021 08:00:43: 17000000 INFO @ Sat, 11 Dec 2021 08:00:45: 16000000 INFO @ Sat, 11 Dec 2021 08:00:45: 9000000 INFO @ Sat, 11 Dec 2021 08:00:50: 18000000 INFO @ Sat, 11 Dec 2021 08:00:51: 17000000 INFO @ Sat, 11 Dec 2021 08:00:53: 10000000 INFO @ Sat, 11 Dec 2021 08:00:57: 18000000 INFO @ Sat, 11 Dec 2021 08:00:58: 19000000 INFO @ Sat, 11 Dec 2021 08:01:00: 11000000 INFO @ Sat, 11 Dec 2021 08:01:03: 19000000 INFO @ Sat, 11 Dec 2021 08:01:05: 20000000 INFO @ Sat, 11 Dec 2021 08:01:08: 12000000 INFO @ Sat, 11 Dec 2021 08:01:09: 20000000 INFO @ Sat, 11 Dec 2021 08:01:13: 21000000 INFO @ Sat, 11 Dec 2021 08:01:15: 13000000 INFO @ Sat, 11 Dec 2021 08:01:16: 21000000 INFO @ Sat, 11 Dec 2021 08:01:20: 22000000 INFO @ Sat, 11 Dec 2021 08:01:22: 22000000 INFO @ Sat, 11 Dec 2021 08:01:22: 14000000 INFO @ Sat, 11 Dec 2021 08:01:27: 23000000 INFO @ Sat, 11 Dec 2021 08:01:29: 23000000 INFO @ Sat, 11 Dec 2021 08:01:30: 15000000 INFO @ Sat, 11 Dec 2021 08:01:35: 24000000 INFO @ Sat, 11 Dec 2021 08:01:36: 24000000 INFO @ Sat, 11 Dec 2021 08:01:37: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:01:37: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:01:37: #1 total tags in treatment: 10927865 INFO @ Sat, 11 Dec 2021 08:01:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:37: #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 08:01:37: #1 tags after filtering in treatment: 10504598 INFO @ Sat, 11 Dec 2021 08:01:37: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 08:01:37: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:37: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:01:37: 16000000 INFO @ Sat, 11 Dec 2021 08:01:37: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:01:37: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:01:37: #1 total tags in treatment: 10927865 INFO @ Sat, 11 Dec 2021 08:01:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:37: #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 08:01:37: #1 tags after filtering in treatment: 10504598 INFO @ Sat, 11 Dec 2021 08:01:37: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 08:01:37: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:01:37: #2 number of paired peaks: 111 WARNING @ Sat, 11 Dec 2021 08:01:37: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Sat, 11 Dec 2021 08:01:37: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:37: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:37: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:37: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:37: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 08:01:37: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 08:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.05_model.r WARNING @ Sat, 11 Dec 2021 08:01:37: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:01:37: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sat, 11 Dec 2021 08:01:37: #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 08:01:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:38: #2 number of paired peaks: 111 WARNING @ Sat, 11 Dec 2021 08:01:38: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Sat, 11 Dec 2021 08:01:38: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:38: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:38: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:38: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:38: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 08:01:38: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 08:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.10_model.r WARNING @ Sat, 11 Dec 2021 08:01:38: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:01:38: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sat, 11 Dec 2021 08:01:38: #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 08:01:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:44: 17000000 INFO @ Sat, 11 Dec 2021 08:01:51: 18000000 INFO @ Sat, 11 Dec 2021 08:01:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:01:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:01:59: 19000000 INFO @ Sat, 11 Dec 2021 08:02:06: 20000000 INFO @ Sat, 11 Dec 2021 08:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.05_summits.bed INFO @ Sat, 11 Dec 2021 08:02:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1357 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.10_summits.bed INFO @ Sat, 11 Dec 2021 08:02:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (691 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:02:13: 21000000 INFO @ Sat, 11 Dec 2021 08:02:20: 22000000 INFO @ Sat, 11 Dec 2021 08:02:27: 23000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:02:34: 24000000 INFO @ Sat, 11 Dec 2021 08:02:36: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:02:36: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:02:36: #1 total tags in treatment: 10927865 INFO @ Sat, 11 Dec 2021 08:02:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:02:36: #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 08:02:36: #1 tags after filtering in treatment: 10504598 INFO @ Sat, 11 Dec 2021 08:02:36: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 08:02:36: #1 finished! INFO @ Sat, 11 Dec 2021 08:02:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:02:37: #2 number of paired peaks: 111 WARNING @ Sat, 11 Dec 2021 08:02:37: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Sat, 11 Dec 2021 08:02:37: start model_add_line... INFO @ Sat, 11 Dec 2021 08:02:37: start X-correlation... INFO @ Sat, 11 Dec 2021 08:02:37: end of X-cor INFO @ Sat, 11 Dec 2021 08:02:37: #2 finished! INFO @ Sat, 11 Dec 2021 08:02:37: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 08:02:37: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 08:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.20_model.r WARNING @ Sat, 11 Dec 2021 08:02:37: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:02:37: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sat, 11 Dec 2021 08:02:37: #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 08:02:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:02:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497045/SRX8497045.20_summits.bed INFO @ Sat, 11 Dec 2021 08:03:07: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling