Job ID = 12265247 SRX = SRX4664626 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27395000 spots for SRR7813053/SRR7813053.sra Written 27395000 spots for SRR7813053/SRR7813053.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265590 ("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: 00:54:34 27395000 reads; of these: 27395000 (100.00%) were paired; of these: 7237432 (26.42%) aligned concordantly 0 times 10326999 (37.70%) aligned concordantly exactly 1 time 9830569 (35.88%) aligned concordantly >1 times ---- 7237432 pairs aligned concordantly 0 times; of these: 2345388 (32.41%) aligned discordantly 1 time ---- 4892044 pairs aligned 0 times concordantly or discordantly; of these: 9784088 mates make up the pairs; of these: 6497670 (66.41%) aligned 0 times 910622 (9.31%) aligned exactly 1 time 2375796 (24.28%) aligned >1 times 88.14% overall alignment rate Time searching: 00:54:34 Overall time: 00:54:34 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] 5912451 / 22196305 = 0.2664 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 07:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.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 07:29:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:29:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:29:20: 1000000 INFO @ Sat, 03 Apr 2021 07:29:28: 2000000 INFO @ Sat, 03 Apr 2021 07:29:36: 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 07:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.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 07:29:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:29:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:29:44: 4000000 INFO @ Sat, 03 Apr 2021 07:29:52: 5000000 INFO @ Sat, 03 Apr 2021 07:29:53: 1000000 INFO @ Sat, 03 Apr 2021 07:30:00: 6000000 INFO @ Sat, 03 Apr 2021 07:30:05: 2000000 INFO @ Sat, 03 Apr 2021 07:30:09: 7000000 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 07:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.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 07:30:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:30:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:30:16: 3000000 INFO @ Sat, 03 Apr 2021 07:30:17: 8000000 INFO @ Sat, 03 Apr 2021 07:30:21: 1000000 INFO @ Sat, 03 Apr 2021 07:30:25: 9000000 INFO @ Sat, 03 Apr 2021 07:30:28: 4000000 INFO @ Sat, 03 Apr 2021 07:30:31: 2000000 INFO @ Sat, 03 Apr 2021 07:30:34: 10000000 INFO @ Sat, 03 Apr 2021 07:30:40: 5000000 INFO @ Sat, 03 Apr 2021 07:30:41: 3000000 INFO @ Sat, 03 Apr 2021 07:30:42: 11000000 INFO @ Sat, 03 Apr 2021 07:30:51: 12000000 INFO @ Sat, 03 Apr 2021 07:30:51: 4000000 INFO @ Sat, 03 Apr 2021 07:30:52: 6000000 INFO @ Sat, 03 Apr 2021 07:31:00: 13000000 INFO @ Sat, 03 Apr 2021 07:31:01: 5000000 INFO @ Sat, 03 Apr 2021 07:31:04: 7000000 INFO @ Sat, 03 Apr 2021 07:31:09: 14000000 INFO @ Sat, 03 Apr 2021 07:31:11: 6000000 INFO @ Sat, 03 Apr 2021 07:31:16: 8000000 INFO @ Sat, 03 Apr 2021 07:31:17: 15000000 INFO @ Sat, 03 Apr 2021 07:31:21: 7000000 INFO @ Sat, 03 Apr 2021 07:31:27: 16000000 INFO @ Sat, 03 Apr 2021 07:31:28: 9000000 INFO @ Sat, 03 Apr 2021 07:31:31: 8000000 INFO @ Sat, 03 Apr 2021 07:31:35: 17000000 INFO @ Sat, 03 Apr 2021 07:31:40: 10000000 INFO @ Sat, 03 Apr 2021 07:31:41: 9000000 INFO @ Sat, 03 Apr 2021 07:31:45: 18000000 INFO @ Sat, 03 Apr 2021 07:31:51: 10000000 INFO @ Sat, 03 Apr 2021 07:31:52: 11000000 INFO @ Sat, 03 Apr 2021 07:31:54: 19000000 INFO @ Sat, 03 Apr 2021 07:32:01: 11000000 INFO @ Sat, 03 Apr 2021 07:32:03: 20000000 INFO @ Sat, 03 Apr 2021 07:32:04: 12000000 INFO @ Sat, 03 Apr 2021 07:32:11: 12000000 INFO @ Sat, 03 Apr 2021 07:32:12: 21000000 INFO @ Sat, 03 Apr 2021 07:32:16: 13000000 INFO @ Sat, 03 Apr 2021 07:32:21: 22000000 INFO @ Sat, 03 Apr 2021 07:32:22: 13000000 INFO @ Sat, 03 Apr 2021 07:32:28: 14000000 INFO @ Sat, 03 Apr 2021 07:32:30: 23000000 INFO @ Sat, 03 Apr 2021 07:32:32: 14000000 INFO @ Sat, 03 Apr 2021 07:32:39: 24000000 INFO @ Sat, 03 Apr 2021 07:32:40: 15000000 INFO @ Sat, 03 Apr 2021 07:32:42: 15000000 INFO @ Sat, 03 Apr 2021 07:32:48: 25000000 INFO @ Sat, 03 Apr 2021 07:32:52: 16000000 INFO @ Sat, 03 Apr 2021 07:32:52: 16000000 INFO @ Sat, 03 Apr 2021 07:32:57: 26000000 INFO @ Sat, 03 Apr 2021 07:33:03: 17000000 INFO @ Sat, 03 Apr 2021 07:33:04: 17000000 INFO @ Sat, 03 Apr 2021 07:33:06: 27000000 INFO @ Sat, 03 Apr 2021 07:33:13: 18000000 INFO @ Sat, 03 Apr 2021 07:33:15: 28000000 INFO @ Sat, 03 Apr 2021 07:33:17: 18000000 INFO @ Sat, 03 Apr 2021 07:33:23: 19000000 INFO @ Sat, 03 Apr 2021 07:33:24: 29000000 INFO @ Sat, 03 Apr 2021 07:33:30: 19000000 INFO @ Sat, 03 Apr 2021 07:33:33: 30000000 INFO @ Sat, 03 Apr 2021 07:33:33: 20000000 INFO @ Sat, 03 Apr 2021 07:33:42: 20000000 INFO @ Sat, 03 Apr 2021 07:33:42: 31000000 INFO @ Sat, 03 Apr 2021 07:33:45: 21000000 INFO @ Sat, 03 Apr 2021 07:33:51: 32000000 INFO @ Sat, 03 Apr 2021 07:33:54: 21000000 INFO @ Sat, 03 Apr 2021 07:33:55: 22000000 INFO @ Sat, 03 Apr 2021 07:34:00: 33000000 INFO @ Sat, 03 Apr 2021 07:34:05: 23000000 INFO @ Sat, 03 Apr 2021 07:34:06: 22000000 INFO @ Sat, 03 Apr 2021 07:34:08: 34000000 INFO @ Sat, 03 Apr 2021 07:34:14: 24000000 INFO @ Sat, 03 Apr 2021 07:34:17: 35000000 INFO @ Sat, 03 Apr 2021 07:34:18: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:34:24: 25000000 INFO @ Sat, 03 Apr 2021 07:34:25: 36000000 INFO @ Sat, 03 Apr 2021 07:34:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:34:29: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:34:29: #1 total tags in treatment: 14512025 INFO @ Sat, 03 Apr 2021 07:34:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:34:29: #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 07:34:30: #1 tags after filtering in treatment: 11361267 INFO @ Sat, 03 Apr 2021 07:34:30: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 07:34:30: #1 finished! INFO @ Sat, 03 Apr 2021 07:34:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:34:30: 24000000 INFO @ Sat, 03 Apr 2021 07:34:31: #2 number of paired peaks: 203 WARNING @ Sat, 03 Apr 2021 07:34:31: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 03 Apr 2021 07:34:31: start model_add_line... INFO @ Sat, 03 Apr 2021 07:34:31: start X-correlation... INFO @ Sat, 03 Apr 2021 07:34:31: end of X-cor INFO @ Sat, 03 Apr 2021 07:34:31: #2 finished! INFO @ Sat, 03 Apr 2021 07:34:31: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 07:34:31: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sat, 03 Apr 2021 07:34:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.05_model.r WARNING @ Sat, 03 Apr 2021 07:34:31: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:34:31: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sat, 03 Apr 2021 07:34:31: #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 07:34:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:34:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:34:34: 26000000 INFO @ Sat, 03 Apr 2021 07:34:41: 25000000 INFO @ Sat, 03 Apr 2021 07:34:44: 27000000 INFO @ Sat, 03 Apr 2021 07:34:53: 26000000 INFO @ Sat, 03 Apr 2021 07:34:54: 28000000 INFO @ Sat, 03 Apr 2021 07:35:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:04: 27000000 INFO @ Sat, 03 Apr 2021 07:35:04: 29000000 INFO @ Sat, 03 Apr 2021 07:35:15: 30000000 INFO @ Sat, 03 Apr 2021 07:35:15: 28000000 INFO @ Sat, 03 Apr 2021 07:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.05_summits.bed INFO @ Sat, 03 Apr 2021 07:35:21: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5214 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:35:25: 31000000 INFO @ Sat, 03 Apr 2021 07:35:27: 29000000 INFO @ Sat, 03 Apr 2021 07:35:35: 32000000 INFO @ Sat, 03 Apr 2021 07:35:38: 30000000 INFO @ Sat, 03 Apr 2021 07:35:45: 33000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:35:50: 31000000 INFO @ Sat, 03 Apr 2021 07:35:56: 34000000 INFO @ Sat, 03 Apr 2021 07:36:01: 32000000 INFO @ Sat, 03 Apr 2021 07:36:06: 35000000 INFO @ Sat, 03 Apr 2021 07:36:12: 33000000 INFO @ Sat, 03 Apr 2021 07:36:16: 36000000 INFO @ Sat, 03 Apr 2021 07:36:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:36:20: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:36:20: #1 total tags in treatment: 14512025 INFO @ Sat, 03 Apr 2021 07:36:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:20: #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 07:36:21: #1 tags after filtering in treatment: 11361267 INFO @ Sat, 03 Apr 2021 07:36:21: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 07:36:21: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:22: #2 number of paired peaks: 203 WARNING @ Sat, 03 Apr 2021 07:36:22: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 03 Apr 2021 07:36:22: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:22: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:22: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:22: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:22: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 07:36:22: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sat, 03 Apr 2021 07:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.20_model.r WARNING @ Sat, 03 Apr 2021 07:36:22: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:22: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sat, 03 Apr 2021 07:36:22: #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 07:36:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:36:23: 34000000 INFO @ Sat, 03 Apr 2021 07:36:34: 35000000 INFO @ Sat, 03 Apr 2021 07:36:44: 36000000 INFO @ Sat, 03 Apr 2021 07:36:49: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:36:49: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:36:49: #1 total tags in treatment: 14512025 INFO @ Sat, 03 Apr 2021 07:36:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:49: #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 07:36:49: #1 tags after filtering in treatment: 11361267 INFO @ Sat, 03 Apr 2021 07:36:49: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 07:36:49: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:50: #2 number of paired peaks: 203 WARNING @ Sat, 03 Apr 2021 07:36:50: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 03 Apr 2021 07:36:50: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:50: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:50: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:50: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:50: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 07:36:50: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sat, 03 Apr 2021 07:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.10_model.r WARNING @ Sat, 03 Apr 2021 07:36:50: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:50: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sat, 03 Apr 2021 07:36:50: #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 07:36:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:36:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.20_summits.bed INFO @ Sat, 03 Apr 2021 07:37:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (629 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664626/SRX4664626.10_summits.bed INFO @ Sat, 03 Apr 2021 07:37:40: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2169 records, 4 fields): 9 millis CompletedMACS2peakCalling