Job ID = 14167200 SRX = SRX8913805 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26319438 spots for SRR12417804/SRR12417804.sra Written 26319438 spots for SRR12417804/SRR12417804.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168408 ("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: 02:46:57 26319438 reads; of these: 26319438 (100.00%) were paired; of these: 12317321 (46.80%) aligned concordantly 0 times 7080975 (26.90%) aligned concordantly exactly 1 time 6921142 (26.30%) aligned concordantly >1 times ---- 12317321 pairs aligned concordantly 0 times; of these: 3835180 (31.14%) aligned discordantly 1 time ---- 8482141 pairs aligned 0 times concordantly or discordantly; of these: 16964282 mates make up the pairs; of these: 12899983 (76.04%) aligned 0 times 789966 (4.66%) aligned exactly 1 time 3274333 (19.30%) aligned >1 times 75.49% overall alignment rate Time searching: 02:46:57 Overall time: 02:46:57 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 32 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] 3534566 / 17505188 = 0.2019 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 @ Fri, 10 Dec 2021 14:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.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 @ Fri, 10 Dec 2021 14:04:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:04:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:04:56: 1000000 INFO @ Fri, 10 Dec 2021 14:05:04: 2000000 INFO @ Fri, 10 Dec 2021 14:05:11: 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 @ Fri, 10 Dec 2021 14:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.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 @ Fri, 10 Dec 2021 14:05:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:05:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:05:19: 4000000 INFO @ Fri, 10 Dec 2021 14:05:25: 1000000 INFO @ Fri, 10 Dec 2021 14:05:27: 5000000 INFO @ Fri, 10 Dec 2021 14:05:31: 2000000 INFO @ Fri, 10 Dec 2021 14:05:34: 6000000 INFO @ Fri, 10 Dec 2021 14:05:37: 3000000 INFO @ Fri, 10 Dec 2021 14:05:42: 7000000 INFO @ Fri, 10 Dec 2021 14:05:44: 4000000 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 @ Fri, 10 Dec 2021 14:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.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 @ Fri, 10 Dec 2021 14:05:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:05:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:05:50: 8000000 INFO @ Fri, 10 Dec 2021 14:05:50: 5000000 INFO @ Fri, 10 Dec 2021 14:05:55: 1000000 INFO @ Fri, 10 Dec 2021 14:05:56: 6000000 INFO @ Fri, 10 Dec 2021 14:05:58: 9000000 INFO @ Fri, 10 Dec 2021 14:06:01: 2000000 INFO @ Fri, 10 Dec 2021 14:06:03: 7000000 INFO @ Fri, 10 Dec 2021 14:06:05: 10000000 INFO @ Fri, 10 Dec 2021 14:06:08: 3000000 INFO @ Fri, 10 Dec 2021 14:06:09: 8000000 INFO @ Fri, 10 Dec 2021 14:06:13: 11000000 INFO @ Fri, 10 Dec 2021 14:06:14: 4000000 INFO @ Fri, 10 Dec 2021 14:06:15: 9000000 INFO @ Fri, 10 Dec 2021 14:06:20: 5000000 INFO @ Fri, 10 Dec 2021 14:06:21: 12000000 INFO @ Fri, 10 Dec 2021 14:06:21: 10000000 INFO @ Fri, 10 Dec 2021 14:06:26: 6000000 INFO @ Fri, 10 Dec 2021 14:06:28: 11000000 INFO @ Fri, 10 Dec 2021 14:06:29: 13000000 INFO @ Fri, 10 Dec 2021 14:06:33: 7000000 INFO @ Fri, 10 Dec 2021 14:06:34: 12000000 INFO @ Fri, 10 Dec 2021 14:06:36: 14000000 INFO @ Fri, 10 Dec 2021 14:06:39: 8000000 INFO @ Fri, 10 Dec 2021 14:06:40: 13000000 INFO @ Fri, 10 Dec 2021 14:06:44: 15000000 INFO @ Fri, 10 Dec 2021 14:06:45: 9000000 INFO @ Fri, 10 Dec 2021 14:06:47: 14000000 INFO @ Fri, 10 Dec 2021 14:06:52: 10000000 INFO @ Fri, 10 Dec 2021 14:06:52: 16000000 INFO @ Fri, 10 Dec 2021 14:06:53: 15000000 INFO @ Fri, 10 Dec 2021 14:06:58: 11000000 INFO @ Fri, 10 Dec 2021 14:06:59: 16000000 INFO @ Fri, 10 Dec 2021 14:07:00: 17000000 INFO @ Fri, 10 Dec 2021 14:07:04: 12000000 INFO @ Fri, 10 Dec 2021 14:07:05: 17000000 INFO @ Fri, 10 Dec 2021 14:07:07: 18000000 INFO @ Fri, 10 Dec 2021 14:07:11: 13000000 INFO @ Fri, 10 Dec 2021 14:07:12: 18000000 INFO @ Fri, 10 Dec 2021 14:07:15: 19000000 INFO @ Fri, 10 Dec 2021 14:07:17: 14000000 INFO @ Fri, 10 Dec 2021 14:07:18: 19000000 INFO @ Fri, 10 Dec 2021 14:07:23: 20000000 INFO @ Fri, 10 Dec 2021 14:07:23: 15000000 INFO @ Fri, 10 Dec 2021 14:07:25: 20000000 INFO @ Fri, 10 Dec 2021 14:07:29: 16000000 INFO @ Fri, 10 Dec 2021 14:07:31: 21000000 INFO @ Fri, 10 Dec 2021 14:07:32: 21000000 INFO @ Fri, 10 Dec 2021 14:07:36: 17000000 INFO @ Fri, 10 Dec 2021 14:07:39: 22000000 INFO @ Fri, 10 Dec 2021 14:07:40: 22000000 INFO @ Fri, 10 Dec 2021 14:07:42: 18000000 INFO @ Fri, 10 Dec 2021 14:07:47: 23000000 INFO @ Fri, 10 Dec 2021 14:07:47: 23000000 INFO @ Fri, 10 Dec 2021 14:07:48: 19000000 INFO @ Fri, 10 Dec 2021 14:07:55: 20000000 INFO @ Fri, 10 Dec 2021 14:07:55: 24000000 INFO @ Fri, 10 Dec 2021 14:07:55: 24000000 INFO @ Fri, 10 Dec 2021 14:08:01: 21000000 INFO @ Fri, 10 Dec 2021 14:08:03: 25000000 INFO @ Fri, 10 Dec 2021 14:08:03: 25000000 INFO @ Fri, 10 Dec 2021 14:08:08: 22000000 INFO @ Fri, 10 Dec 2021 14:08:11: 26000000 INFO @ Fri, 10 Dec 2021 14:08:11: 26000000 INFO @ Fri, 10 Dec 2021 14:08:14: 23000000 INFO @ Fri, 10 Dec 2021 14:08:19: 27000000 INFO @ Fri, 10 Dec 2021 14:08:19: 27000000 INFO @ Fri, 10 Dec 2021 14:08:21: 24000000 INFO @ Fri, 10 Dec 2021 14:08:27: 28000000 INFO @ Fri, 10 Dec 2021 14:08:27: 25000000 INFO @ Fri, 10 Dec 2021 14:08:28: 28000000 INFO @ Fri, 10 Dec 2021 14:08:34: 26000000 INFO @ Fri, 10 Dec 2021 14:08:35: 29000000 INFO @ Fri, 10 Dec 2021 14:08:36: 29000000 INFO @ Fri, 10 Dec 2021 14:08:40: 27000000 INFO @ Fri, 10 Dec 2021 14:08:44: 30000000 INFO @ Fri, 10 Dec 2021 14:08:44: 30000000 INFO @ Fri, 10 Dec 2021 14:08:47: 28000000 INFO @ Fri, 10 Dec 2021 14:08:52: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:08:52: 31000000 INFO @ Fri, 10 Dec 2021 14:08:54: 29000000 INFO @ Fri, 10 Dec 2021 14:08:59: 32000000 INFO @ Fri, 10 Dec 2021 14:09:00: 32000000 INFO @ Fri, 10 Dec 2021 14:09:01: 30000000 INFO @ Fri, 10 Dec 2021 14:09:05: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 14:09:05: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 14:09:05: #1 total tags in treatment: 10830874 INFO @ Fri, 10 Dec 2021 14:09:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:09:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:09:05: #1 tags after filtering in treatment: 8662793 INFO @ Fri, 10 Dec 2021 14:09:05: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Dec 2021 14:09:05: #1 finished! INFO @ Fri, 10 Dec 2021 14:09:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:09:05: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 14:09:05: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 14:09:05: #1 total tags in treatment: 10830874 INFO @ Fri, 10 Dec 2021 14:09:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:09:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:09:05: #1 tags after filtering in treatment: 8662793 INFO @ Fri, 10 Dec 2021 14:09:05: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Dec 2021 14:09:05: #1 finished! INFO @ Fri, 10 Dec 2021 14:09:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:09:05: #2 number of paired peaks: 612 WARNING @ Fri, 10 Dec 2021 14:09:05: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Fri, 10 Dec 2021 14:09:05: start model_add_line... INFO @ Fri, 10 Dec 2021 14:09:06: start X-correlation... INFO @ Fri, 10 Dec 2021 14:09:06: end of X-cor INFO @ Fri, 10 Dec 2021 14:09:06: #2 finished! INFO @ Fri, 10 Dec 2021 14:09:06: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 14:09:06: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 14:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.05_model.r WARNING @ Fri, 10 Dec 2021 14:09:06: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:09:06: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 10 Dec 2021 14:09:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:09:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:09:06: #2 number of paired peaks: 612 WARNING @ Fri, 10 Dec 2021 14:09:06: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Fri, 10 Dec 2021 14:09:06: start model_add_line... INFO @ Fri, 10 Dec 2021 14:09:06: start X-correlation... INFO @ Fri, 10 Dec 2021 14:09:06: end of X-cor INFO @ Fri, 10 Dec 2021 14:09:06: #2 finished! INFO @ Fri, 10 Dec 2021 14:09:06: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 14:09:06: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 14:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.10_model.r WARNING @ Fri, 10 Dec 2021 14:09:06: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:09:06: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 10 Dec 2021 14:09:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:09:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:09:07: 31000000 INFO @ Fri, 10 Dec 2021 14:09:13: 32000000 INFO @ Fri, 10 Dec 2021 14:09:17: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 14:09:17: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 14:09:17: #1 total tags in treatment: 10830874 INFO @ Fri, 10 Dec 2021 14:09:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:09:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:09:18: #1 tags after filtering in treatment: 8662793 INFO @ Fri, 10 Dec 2021 14:09:18: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 10 Dec 2021 14:09:18: #1 finished! INFO @ Fri, 10 Dec 2021 14:09:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:09:18: #2 number of paired peaks: 612 WARNING @ Fri, 10 Dec 2021 14:09:18: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Fri, 10 Dec 2021 14:09:18: start model_add_line... INFO @ Fri, 10 Dec 2021 14:09:18: start X-correlation... INFO @ Fri, 10 Dec 2021 14:09:18: end of X-cor INFO @ Fri, 10 Dec 2021 14:09:18: #2 finished! INFO @ Fri, 10 Dec 2021 14:09:18: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 14:09:18: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 14:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.20_model.r WARNING @ Fri, 10 Dec 2021 14:09:18: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:09:18: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 10 Dec 2021 14:09:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:09:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:09:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:09:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:09:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:09:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:09:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.05_summits.bed INFO @ Fri, 10 Dec 2021 14:09:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3504 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.10_summits.bed INFO @ Fri, 10 Dec 2021 14:09:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1855 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:09:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:09:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:09:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:09:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913805/SRX8913805.20_summits.bed INFO @ Fri, 10 Dec 2021 14:09:44: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (986 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。