Job ID = 14167080 SRX = SRX4712922 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21264570 spots for SRR7874052/SRR7874052.sra Written 21264570 spots for SRR7874052/SRR7874052.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167582 ("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: 00:41:10 21264570 reads; of these: 21264570 (100.00%) were paired; of these: 4765241 (22.41%) aligned concordantly 0 times 11389019 (53.56%) aligned concordantly exactly 1 time 5110310 (24.03%) aligned concordantly >1 times ---- 4765241 pairs aligned concordantly 0 times; of these: 2226449 (46.72%) aligned discordantly 1 time ---- 2538792 pairs aligned 0 times concordantly or discordantly; of these: 5077584 mates make up the pairs; of these: 3083119 (60.72%) aligned 0 times 679885 (13.39%) aligned exactly 1 time 1314580 (25.89%) aligned >1 times 92.75% overall alignment rate Time searching: 00:41:10 Overall time: 00:41:10 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] 1227486 / 18549341 = 0.0662 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 10:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.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 10:33:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:33:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:33:50: 1000000 INFO @ Fri, 10 Dec 2021 10:33:57: 2000000 INFO @ Fri, 10 Dec 2021 10:34:05: 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 10:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.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 10:34:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:34:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:34:12: 4000000 INFO @ Fri, 10 Dec 2021 10:34:21: 1000000 INFO @ Fri, 10 Dec 2021 10:34:21: 5000000 INFO @ Fri, 10 Dec 2021 10:34:29: 2000000 INFO @ Fri, 10 Dec 2021 10:34:29: 6000000 INFO @ Fri, 10 Dec 2021 10:34:38: 3000000 INFO @ Fri, 10 Dec 2021 10:34:38: 7000000 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 10:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.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 10:34:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:34:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:34:46: 4000000 INFO @ Fri, 10 Dec 2021 10:34:46: 8000000 INFO @ Fri, 10 Dec 2021 10:34:51: 1000000 INFO @ Fri, 10 Dec 2021 10:34:55: 9000000 INFO @ Fri, 10 Dec 2021 10:34:55: 5000000 INFO @ Fri, 10 Dec 2021 10:35:00: 2000000 INFO @ Fri, 10 Dec 2021 10:35:04: 10000000 INFO @ Fri, 10 Dec 2021 10:35:04: 6000000 INFO @ Fri, 10 Dec 2021 10:35:09: 3000000 INFO @ Fri, 10 Dec 2021 10:35:12: 11000000 INFO @ Fri, 10 Dec 2021 10:35:13: 7000000 INFO @ Fri, 10 Dec 2021 10:35:18: 4000000 INFO @ Fri, 10 Dec 2021 10:35:21: 12000000 INFO @ Fri, 10 Dec 2021 10:35:22: 8000000 INFO @ Fri, 10 Dec 2021 10:35:27: 5000000 INFO @ Fri, 10 Dec 2021 10:35:30: 13000000 INFO @ Fri, 10 Dec 2021 10:35:31: 9000000 INFO @ Fri, 10 Dec 2021 10:35:36: 6000000 INFO @ Fri, 10 Dec 2021 10:35:38: 14000000 INFO @ Fri, 10 Dec 2021 10:35:40: 10000000 INFO @ Fri, 10 Dec 2021 10:35:45: 7000000 INFO @ Fri, 10 Dec 2021 10:35:47: 15000000 INFO @ Fri, 10 Dec 2021 10:35:49: 11000000 INFO @ Fri, 10 Dec 2021 10:35:54: 8000000 INFO @ Fri, 10 Dec 2021 10:35:56: 16000000 INFO @ Fri, 10 Dec 2021 10:35:58: 12000000 INFO @ Fri, 10 Dec 2021 10:36:03: 9000000 INFO @ Fri, 10 Dec 2021 10:36:04: 17000000 INFO @ Fri, 10 Dec 2021 10:36:07: 13000000 INFO @ Fri, 10 Dec 2021 10:36:12: 10000000 INFO @ Fri, 10 Dec 2021 10:36:13: 18000000 INFO @ Fri, 10 Dec 2021 10:36:16: 14000000 INFO @ Fri, 10 Dec 2021 10:36:21: 11000000 INFO @ Fri, 10 Dec 2021 10:36:22: 19000000 INFO @ Fri, 10 Dec 2021 10:36:25: 15000000 INFO @ Fri, 10 Dec 2021 10:36:30: 12000000 INFO @ Fri, 10 Dec 2021 10:36:30: 20000000 INFO @ Fri, 10 Dec 2021 10:36:34: 16000000 INFO @ Fri, 10 Dec 2021 10:36:38: 13000000 INFO @ Fri, 10 Dec 2021 10:36:39: 21000000 INFO @ Fri, 10 Dec 2021 10:36:42: 17000000 INFO @ Fri, 10 Dec 2021 10:36:47: 14000000 INFO @ Fri, 10 Dec 2021 10:36:47: 22000000 INFO @ Fri, 10 Dec 2021 10:36:51: 18000000 INFO @ Fri, 10 Dec 2021 10:36:55: 15000000 INFO @ Fri, 10 Dec 2021 10:36:55: 23000000 INFO @ Fri, 10 Dec 2021 10:37:00: 19000000 INFO @ Fri, 10 Dec 2021 10:37:04: 16000000 INFO @ Fri, 10 Dec 2021 10:37:04: 24000000 INFO @ Fri, 10 Dec 2021 10:37:09: 20000000 INFO @ Fri, 10 Dec 2021 10:37:13: 25000000 INFO @ Fri, 10 Dec 2021 10:37:13: 17000000 INFO @ Fri, 10 Dec 2021 10:37:17: 21000000 INFO @ Fri, 10 Dec 2021 10:37:21: 26000000 INFO @ Fri, 10 Dec 2021 10:37:21: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:37:26: 22000000 INFO @ Fri, 10 Dec 2021 10:37:29: 27000000 INFO @ Fri, 10 Dec 2021 10:37:30: 19000000 INFO @ Fri, 10 Dec 2021 10:37:35: 23000000 INFO @ Fri, 10 Dec 2021 10:37:38: 28000000 INFO @ Fri, 10 Dec 2021 10:37:39: 20000000 INFO @ Fri, 10 Dec 2021 10:37:43: 24000000 INFO @ Fri, 10 Dec 2021 10:37:46: 29000000 INFO @ Fri, 10 Dec 2021 10:37:47: 21000000 INFO @ Fri, 10 Dec 2021 10:37:52: 25000000 INFO @ Fri, 10 Dec 2021 10:37:55: 30000000 INFO @ Fri, 10 Dec 2021 10:37:56: 22000000 INFO @ Fri, 10 Dec 2021 10:38:01: 26000000 INFO @ Fri, 10 Dec 2021 10:38:03: 31000000 INFO @ Fri, 10 Dec 2021 10:38:04: 23000000 INFO @ Fri, 10 Dec 2021 10:38:09: 27000000 INFO @ Fri, 10 Dec 2021 10:38:12: 32000000 INFO @ Fri, 10 Dec 2021 10:38:13: 24000000 INFO @ Fri, 10 Dec 2021 10:38:18: 28000000 INFO @ Fri, 10 Dec 2021 10:38:21: 33000000 INFO @ Fri, 10 Dec 2021 10:38:21: 25000000 INFO @ Fri, 10 Dec 2021 10:38:27: 29000000 INFO @ Fri, 10 Dec 2021 10:38:29: 34000000 INFO @ Fri, 10 Dec 2021 10:38:30: 26000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:38:36: 30000000 INFO @ Fri, 10 Dec 2021 10:38:37: 35000000 INFO @ Fri, 10 Dec 2021 10:38:38: 27000000 INFO @ Fri, 10 Dec 2021 10:38:44: 31000000 INFO @ Fri, 10 Dec 2021 10:38:46: 36000000 INFO @ Fri, 10 Dec 2021 10:38:47: 28000000 INFO @ Fri, 10 Dec 2021 10:38:53: 32000000 INFO @ Fri, 10 Dec 2021 10:38:54: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:38:54: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:38:54: #1 total tags in treatment: 15308902 INFO @ Fri, 10 Dec 2021 10:38:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:38:54: #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 10:38:54: #1 tags after filtering in treatment: 12636931 INFO @ Fri, 10 Dec 2021 10:38:54: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Dec 2021 10:38:54: #1 finished! INFO @ Fri, 10 Dec 2021 10:38:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:38:55: #2 number of paired peaks: 117 WARNING @ Fri, 10 Dec 2021 10:38:55: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Fri, 10 Dec 2021 10:38:55: start model_add_line... INFO @ Fri, 10 Dec 2021 10:38:55: start X-correlation... INFO @ Fri, 10 Dec 2021 10:38:55: end of X-cor INFO @ Fri, 10 Dec 2021 10:38:55: #2 finished! INFO @ Fri, 10 Dec 2021 10:38:55: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 10:38:55: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 10:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.05_model.r INFO @ Fri, 10 Dec 2021 10:38:55: 29000000 WARNING @ Fri, 10 Dec 2021 10:38:56: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:38:56: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 10:38:56: #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 10:38:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:38:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:39:02: 33000000 INFO @ Fri, 10 Dec 2021 10:39:04: 30000000 INFO @ Fri, 10 Dec 2021 10:39:11: 34000000 INFO @ Fri, 10 Dec 2021 10:39:12: 31000000 INFO @ Fri, 10 Dec 2021 10:39:19: 35000000 INFO @ Fri, 10 Dec 2021 10:39:21: 32000000 INFO @ Fri, 10 Dec 2021 10:39:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:39:28: 36000000 INFO @ Fri, 10 Dec 2021 10:39:29: 33000000 INFO @ Fri, 10 Dec 2021 10:39:36: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:39:36: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:39:36: #1 total tags in treatment: 15308902 INFO @ Fri, 10 Dec 2021 10:39:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:39:36: #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 10:39:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:39:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:39:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.05_summits.bed INFO @ Fri, 10 Dec 2021 10:39:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5422 records, 4 fields): 7 millis INFO @ Fri, 10 Dec 2021 10:39:37: #1 tags after filtering in treatment: 12636931 INFO @ Fri, 10 Dec 2021 10:39:37: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Dec 2021 10:39:37: #1 finished! INFO @ Fri, 10 Dec 2021 10:39:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:39:37: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:39:38: #2 number of paired peaks: 117 WARNING @ Fri, 10 Dec 2021 10:39:38: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Fri, 10 Dec 2021 10:39:38: start model_add_line... INFO @ Fri, 10 Dec 2021 10:39:38: start X-correlation... INFO @ Fri, 10 Dec 2021 10:39:38: end of X-cor INFO @ Fri, 10 Dec 2021 10:39:38: #2 finished! INFO @ Fri, 10 Dec 2021 10:39:38: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 10:39:38: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 10:39:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.10_model.r WARNING @ Fri, 10 Dec 2021 10:39:38: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:39:38: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 10:39:38: #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 10:39:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:39:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:39:38: 34000000 INFO @ Fri, 10 Dec 2021 10:39:46: 35000000 INFO @ Fri, 10 Dec 2021 10:39:53: 36000000 INFO @ Fri, 10 Dec 2021 10:40:01: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:40:01: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:40:01: #1 total tags in treatment: 15308902 INFO @ Fri, 10 Dec 2021 10:40:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:40:01: #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 10:40:01: #1 tags after filtering in treatment: 12636931 INFO @ Fri, 10 Dec 2021 10:40:01: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Dec 2021 10:40:01: #1 finished! INFO @ Fri, 10 Dec 2021 10:40:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:40:02: #2 number of paired peaks: 117 WARNING @ Fri, 10 Dec 2021 10:40:02: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Fri, 10 Dec 2021 10:40:02: start model_add_line... INFO @ Fri, 10 Dec 2021 10:40:02: start X-correlation... INFO @ Fri, 10 Dec 2021 10:40:02: end of X-cor INFO @ Fri, 10 Dec 2021 10:40:02: #2 finished! INFO @ Fri, 10 Dec 2021 10:40:02: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 10:40:02: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 10:40:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.20_model.r WARNING @ Fri, 10 Dec 2021 10:40:02: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:40:02: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 10:40:02: #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 10:40:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:40:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:40:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.10_summits.bed INFO @ Fri, 10 Dec 2021 10:40:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2054 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:40:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712922/SRX4712922.20_summits.bed INFO @ Fri, 10 Dec 2021 10:40:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (642 records, 4 fields): 2 millis CompletedMACS2peakCalling