Job ID = 14170109 SRX = SRX8556257 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33926842 spots for SRR12024631/SRR12024631.sra Written 33926842 spots for SRR12024631/SRR12024631.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170735 ("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: 00:49:16 33926842 reads; of these: 33926842 (100.00%) were paired; of these: 25318534 (74.63%) aligned concordantly 0 times 7101248 (20.93%) aligned concordantly exactly 1 time 1507060 (4.44%) aligned concordantly >1 times ---- 25318534 pairs aligned concordantly 0 times; of these: 2226164 (8.79%) aligned discordantly 1 time ---- 23092370 pairs aligned 0 times concordantly or discordantly; of these: 46184740 mates make up the pairs; of these: 44243570 (95.80%) aligned 0 times 692691 (1.50%) aligned exactly 1 time 1248479 (2.70%) aligned >1 times 34.80% overall alignment rate Time searching: 00:49:16 Overall time: 00:49:16 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] 1146525 / 10777617 = 0.1064 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 06:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.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 06:30:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:30:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:30:33: 1000000 INFO @ Sat, 11 Dec 2021 06:30:42: 2000000 INFO @ Sat, 11 Dec 2021 06:30:50: 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 06:30:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.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 06:30:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:30:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:30:59: 4000000 INFO @ Sat, 11 Dec 2021 06:31:07: 1000000 INFO @ Sat, 11 Dec 2021 06:31:08: 5000000 INFO @ Sat, 11 Dec 2021 06:31:18: 6000000 INFO @ Sat, 11 Dec 2021 06:31:19: 2000000 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 06:31:28: 7000000 INFO @ Sat, 11 Dec 2021 06:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.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 06:31:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:31:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:31:30: 3000000 INFO @ Sat, 11 Dec 2021 06:31:37: 8000000 INFO @ Sat, 11 Dec 2021 06:31:38: 1000000 INFO @ Sat, 11 Dec 2021 06:31:42: 4000000 INFO @ Sat, 11 Dec 2021 06:31:47: 9000000 INFO @ Sat, 11 Dec 2021 06:31:48: 2000000 INFO @ Sat, 11 Dec 2021 06:31:55: 5000000 INFO @ Sat, 11 Dec 2021 06:31:57: 10000000 INFO @ Sat, 11 Dec 2021 06:31:59: 3000000 INFO @ Sat, 11 Dec 2021 06:32:07: 6000000 INFO @ Sat, 11 Dec 2021 06:32:07: 11000000 INFO @ Sat, 11 Dec 2021 06:32:09: 4000000 INFO @ Sat, 11 Dec 2021 06:32:17: 12000000 INFO @ Sat, 11 Dec 2021 06:32:18: 7000000 INFO @ Sat, 11 Dec 2021 06:32:19: 5000000 INFO @ Sat, 11 Dec 2021 06:32:28: 13000000 INFO @ Sat, 11 Dec 2021 06:32:29: 6000000 INFO @ Sat, 11 Dec 2021 06:32:30: 8000000 INFO @ Sat, 11 Dec 2021 06:32:38: 14000000 INFO @ Sat, 11 Dec 2021 06:32:39: 7000000 INFO @ Sat, 11 Dec 2021 06:32:42: 9000000 INFO @ Sat, 11 Dec 2021 06:32:48: 15000000 INFO @ Sat, 11 Dec 2021 06:32:49: 8000000 INFO @ Sat, 11 Dec 2021 06:32:53: 10000000 INFO @ Sat, 11 Dec 2021 06:32:58: 16000000 INFO @ Sat, 11 Dec 2021 06:32:59: 9000000 INFO @ Sat, 11 Dec 2021 06:33:04: 11000000 INFO @ Sat, 11 Dec 2021 06:33:09: 17000000 INFO @ Sat, 11 Dec 2021 06:33:09: 10000000 INFO @ Sat, 11 Dec 2021 06:33:16: 12000000 INFO @ Sat, 11 Dec 2021 06:33:19: 11000000 INFO @ Sat, 11 Dec 2021 06:33:20: 18000000 INFO @ Sat, 11 Dec 2021 06:33:27: 13000000 INFO @ Sat, 11 Dec 2021 06:33:29: 12000000 INFO @ Sat, 11 Dec 2021 06:33:31: 19000000 INFO @ Sat, 11 Dec 2021 06:33:39: 14000000 INFO @ Sat, 11 Dec 2021 06:33:40: 13000000 INFO @ Sat, 11 Dec 2021 06:33:41: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:33:50: 14000000 INFO @ Sat, 11 Dec 2021 06:33:51: 21000000 INFO @ Sat, 11 Dec 2021 06:33:51: 15000000 INFO @ Sat, 11 Dec 2021 06:33:55: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:33:55: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:33:55: #1 total tags in treatment: 7622511 INFO @ Sat, 11 Dec 2021 06:33:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:33:55: #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 06:33:55: #1 tags after filtering in treatment: 6644247 INFO @ Sat, 11 Dec 2021 06:33:55: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 06:33:55: #1 finished! INFO @ Sat, 11 Dec 2021 06:33:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:33:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:33:55: #2 number of paired peaks: 581 WARNING @ Sat, 11 Dec 2021 06:33:55: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Sat, 11 Dec 2021 06:33:55: start model_add_line... INFO @ Sat, 11 Dec 2021 06:33:55: start X-correlation... INFO @ Sat, 11 Dec 2021 06:33:55: end of X-cor INFO @ Sat, 11 Dec 2021 06:33:55: #2 finished! INFO @ Sat, 11 Dec 2021 06:33:55: #2 predicted fragment length is 246 bps INFO @ Sat, 11 Dec 2021 06:33:55: #2 alternative fragment length(s) may be 246 bps INFO @ Sat, 11 Dec 2021 06:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.05_model.r WARNING @ Sat, 11 Dec 2021 06:33:55: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:33:55: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Sat, 11 Dec 2021 06:33:55: #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 06:33:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:34:01: 15000000 INFO @ Sat, 11 Dec 2021 06:34:03: 16000000 INFO @ Sat, 11 Dec 2021 06:34:10: 16000000 INFO @ Sat, 11 Dec 2021 06:34:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:34:15: 17000000 INFO @ Sat, 11 Dec 2021 06:34:21: 17000000 INFO @ Sat, 11 Dec 2021 06:34:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:34:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:34:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.05_summits.bed INFO @ Sat, 11 Dec 2021 06:34:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4650 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:34:27: 18000000 INFO @ Sat, 11 Dec 2021 06:34:31: 18000000 INFO @ Sat, 11 Dec 2021 06:34:38: 19000000 INFO @ Sat, 11 Dec 2021 06:34:41: 19000000 INFO @ Sat, 11 Dec 2021 06:34:49: 20000000 INFO @ Sat, 11 Dec 2021 06:34:51: 20000000 INFO @ Sat, 11 Dec 2021 06:35:01: 21000000 INFO @ Sat, 11 Dec 2021 06:35:01: 21000000 INFO @ Sat, 11 Dec 2021 06:35:04: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:35:04: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:35:04: #1 total tags in treatment: 7622511 INFO @ Sat, 11 Dec 2021 06:35:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:35:04: #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 06:35:04: #1 tags after filtering in treatment: 6644247 INFO @ Sat, 11 Dec 2021 06:35:04: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 06:35:04: #1 finished! INFO @ Sat, 11 Dec 2021 06:35:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:35:05: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:35:05: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:35:05: #1 total tags in treatment: 7622511 INFO @ Sat, 11 Dec 2021 06:35:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:35:05: #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 06:35:05: #1 tags after filtering in treatment: 6644247 INFO @ Sat, 11 Dec 2021 06:35:05: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 06:35:05: #1 finished! INFO @ Sat, 11 Dec 2021 06:35:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:35:05: #2 number of paired peaks: 581 WARNING @ Sat, 11 Dec 2021 06:35:05: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Sat, 11 Dec 2021 06:35:05: start model_add_line... INFO @ Sat, 11 Dec 2021 06:35:05: start X-correlation... INFO @ Sat, 11 Dec 2021 06:35:05: end of X-cor INFO @ Sat, 11 Dec 2021 06:35:05: #2 finished! INFO @ Sat, 11 Dec 2021 06:35:05: #2 predicted fragment length is 246 bps INFO @ Sat, 11 Dec 2021 06:35:05: #2 alternative fragment length(s) may be 246 bps INFO @ Sat, 11 Dec 2021 06:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.10_model.r WARNING @ Sat, 11 Dec 2021 06:35:05: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:35:05: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Sat, 11 Dec 2021 06:35:05: #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 06:35:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:35:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:35:05: #2 number of paired peaks: 581 WARNING @ Sat, 11 Dec 2021 06:35:05: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Sat, 11 Dec 2021 06:35:05: start model_add_line... INFO @ Sat, 11 Dec 2021 06:35:05: start X-correlation... INFO @ Sat, 11 Dec 2021 06:35:05: end of X-cor INFO @ Sat, 11 Dec 2021 06:35:05: #2 finished! INFO @ Sat, 11 Dec 2021 06:35:05: #2 predicted fragment length is 246 bps INFO @ Sat, 11 Dec 2021 06:35:05: #2 alternative fragment length(s) may be 246 bps INFO @ Sat, 11 Dec 2021 06:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.20_model.r WARNING @ Sat, 11 Dec 2021 06:35:05: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:35:05: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Sat, 11 Dec 2021 06:35:05: #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 06:35:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:35:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:35:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:35:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:35:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:35:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:35:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.20_summits.bed INFO @ Sat, 11 Dec 2021 06:35:32: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:35:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:35:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:35:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556257/SRX8556257.10_summits.bed INFO @ Sat, 11 Dec 2021 06:35:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1975 records, 4 fields): 4 millis CompletedMACS2peakCalling