Job ID = 12266679 SRX = SRX8174041 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12701289 spots for SRR11607682/SRR11607682.sra Written 12701289 spots for SRR11607682/SRR11607682.sra Read 5713446 spots for SRR11607683/SRR11607683.sra Written 5713446 spots for SRR11607683/SRR11607683.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267219 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:37:40 18414735 reads; of these: 18414735 (100.00%) were paired; of these: 1476413 (8.02%) aligned concordantly 0 times 7535439 (40.92%) aligned concordantly exactly 1 time 9402883 (51.06%) aligned concordantly >1 times ---- 1476413 pairs aligned concordantly 0 times; of these: 421868 (28.57%) aligned discordantly 1 time ---- 1054545 pairs aligned 0 times concordantly or discordantly; of these: 2109090 mates make up the pairs; of these: 1211076 (57.42%) aligned 0 times 312240 (14.80%) aligned exactly 1 time 585774 (27.77%) aligned >1 times 96.71% overall alignment rate Time searching: 00:37:41 Overall time: 00:37:41 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] 6099258 / 17210495 = 0.3544 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 09:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.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 09:57:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:57:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:57:33: 1000000 INFO @ Sat, 03 Apr 2021 09:57:43: 2000000 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 09:57:52: 3000000 INFO @ Sat, 03 Apr 2021 09:57:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.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 09:57:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:57:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:58:03: 4000000 INFO @ Sat, 03 Apr 2021 09:58:05: 1000000 INFO @ Sat, 03 Apr 2021 09:58:15: 5000000 INFO @ Sat, 03 Apr 2021 09:58:16: 2000000 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 09:58:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.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 09:58:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:58:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:58:26: 6000000 INFO @ Sat, 03 Apr 2021 09:58:30: 3000000 INFO @ Sat, 03 Apr 2021 09:58:34: 1000000 INFO @ Sat, 03 Apr 2021 09:58:40: 7000000 INFO @ Sat, 03 Apr 2021 09:58:42: 4000000 INFO @ Sat, 03 Apr 2021 09:58:47: 2000000 INFO @ Sat, 03 Apr 2021 09:58:52: 8000000 INFO @ Sat, 03 Apr 2021 09:58:55: 5000000 INFO @ Sat, 03 Apr 2021 09:58:57: 3000000 INFO @ Sat, 03 Apr 2021 09:59:03: 9000000 INFO @ Sat, 03 Apr 2021 09:59:09: 4000000 INFO @ Sat, 03 Apr 2021 09:59:09: 6000000 INFO @ Sat, 03 Apr 2021 09:59:15: 10000000 INFO @ Sat, 03 Apr 2021 09:59:20: 5000000 INFO @ Sat, 03 Apr 2021 09:59:22: 7000000 INFO @ Sat, 03 Apr 2021 09:59:26: 11000000 INFO @ Sat, 03 Apr 2021 09:59:32: 6000000 INFO @ Sat, 03 Apr 2021 09:59:38: 8000000 INFO @ Sat, 03 Apr 2021 09:59:40: 12000000 INFO @ Sat, 03 Apr 2021 09:59:45: 7000000 INFO @ Sat, 03 Apr 2021 09:59:53: 13000000 INFO @ Sat, 03 Apr 2021 09:59:54: 9000000 INFO @ Sat, 03 Apr 2021 09:59:56: 8000000 INFO @ Sat, 03 Apr 2021 10:00:03: 14000000 INFO @ Sat, 03 Apr 2021 10:00:08: 10000000 INFO @ Sat, 03 Apr 2021 10:00:10: 9000000 INFO @ Sat, 03 Apr 2021 10:00:15: 15000000 INFO @ Sat, 03 Apr 2021 10:00:19: 11000000 INFO @ Sat, 03 Apr 2021 10:00:20: 10000000 INFO @ Sat, 03 Apr 2021 10:00:26: 16000000 INFO @ Sat, 03 Apr 2021 10:00:30: 11000000 INFO @ Sat, 03 Apr 2021 10:00:32: 12000000 INFO @ Sat, 03 Apr 2021 10:00:38: 17000000 INFO @ Sat, 03 Apr 2021 10:00:42: 12000000 INFO @ Sat, 03 Apr 2021 10:00:47: 13000000 INFO @ Sat, 03 Apr 2021 10:00:50: 18000000 INFO @ Sat, 03 Apr 2021 10:00:53: 13000000 INFO @ Sat, 03 Apr 2021 10:01:00: 14000000 INFO @ Sat, 03 Apr 2021 10:01:04: 14000000 INFO @ Sat, 03 Apr 2021 10:01:04: 19000000 INFO @ Sat, 03 Apr 2021 10:01:14: 15000000 INFO @ Sat, 03 Apr 2021 10:01:15: 20000000 INFO @ Sat, 03 Apr 2021 10:01:16: 15000000 INFO @ Sat, 03 Apr 2021 10:01:27: 16000000 INFO @ Sat, 03 Apr 2021 10:01:28: 16000000 INFO @ Sat, 03 Apr 2021 10:01:30: 21000000 INFO @ Sat, 03 Apr 2021 10:01:38: 17000000 INFO @ Sat, 03 Apr 2021 10:01:41: 17000000 INFO @ Sat, 03 Apr 2021 10:01:47: 22000000 INFO @ Sat, 03 Apr 2021 10:01:51: 18000000 INFO @ Sat, 03 Apr 2021 10:01:53: 18000000 INFO @ Sat, 03 Apr 2021 10:02:00: 23000000 INFO @ Sat, 03 Apr 2021 10:02:04: 19000000 INFO @ Sat, 03 Apr 2021 10:02:05: 19000000 INFO @ Sat, 03 Apr 2021 10:02:05: #1 tag size is determined as 38 bps INFO @ Sat, 03 Apr 2021 10:02:05: #1 tag size = 38 INFO @ Sat, 03 Apr 2021 10:02:05: #1 total tags in treatment: 10857549 INFO @ Sat, 03 Apr 2021 10:02:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:02:05: #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 10:02:06: #1 tags after filtering in treatment: 8632249 INFO @ Sat, 03 Apr 2021 10:02:06: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 10:02:06: #1 finished! INFO @ Sat, 03 Apr 2021 10:02:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:02:07: #2 number of paired peaks: 522 WARNING @ Sat, 03 Apr 2021 10:02:07: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 03 Apr 2021 10:02:07: start model_add_line... INFO @ Sat, 03 Apr 2021 10:02:07: start X-correlation... INFO @ Sat, 03 Apr 2021 10:02:07: end of X-cor INFO @ Sat, 03 Apr 2021 10:02:07: #2 finished! INFO @ Sat, 03 Apr 2021 10:02:07: #2 predicted fragment length is 66 bps INFO @ Sat, 03 Apr 2021 10:02:07: #2 alternative fragment length(s) may be 4,66 bps INFO @ Sat, 03 Apr 2021 10:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.05_model.r WARNING @ Sat, 03 Apr 2021 10:02:07: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:02:07: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Sat, 03 Apr 2021 10:02:07: #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 10:02:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:02:16: 20000000 INFO @ Sat, 03 Apr 2021 10:02:20: 20000000 INFO @ Sat, 03 Apr 2021 10:02:30: 21000000 INFO @ Sat, 03 Apr 2021 10:02:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:02:33: 21000000 INFO @ Sat, 03 Apr 2021 10:02:43: 22000000 INFO @ Sat, 03 Apr 2021 10:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.05_peaks.xls INFO @ Sat, 03 Apr 2021 10:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.05_summits.bed INFO @ Sat, 03 Apr 2021 10:02:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3830 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:02:46: 22000000 INFO @ Sat, 03 Apr 2021 10:02:57: 23000000 INFO @ Sat, 03 Apr 2021 10:02:58: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 10:03:02: #1 tag size is determined as 38 bps INFO @ Sat, 03 Apr 2021 10:03:02: #1 tag size = 38 INFO @ Sat, 03 Apr 2021 10:03:02: #1 total tags in treatment: 10857549 INFO @ Sat, 03 Apr 2021 10:03:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:03:02: #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 10:03:02: #1 tags after filtering in treatment: 8632249 INFO @ Sat, 03 Apr 2021 10:03:02: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 10:03:02: #1 finished! INFO @ Sat, 03 Apr 2021 10:03:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:03:03: #2 number of paired peaks: 522 WARNING @ Sat, 03 Apr 2021 10:03:03: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 03 Apr 2021 10:03:03: start model_add_line... INFO @ Sat, 03 Apr 2021 10:03:03: #1 tag size is determined as 38 bps INFO @ Sat, 03 Apr 2021 10:03:03: #1 tag size = 38 INFO @ Sat, 03 Apr 2021 10:03:03: #1 total tags in treatment: 10857549 INFO @ Sat, 03 Apr 2021 10:03:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:03:03: start X-correlation... INFO @ Sat, 03 Apr 2021 10:03:03: #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 10:03:03: end of X-cor INFO @ Sat, 03 Apr 2021 10:03:03: #2 finished! INFO @ Sat, 03 Apr 2021 10:03:03: #2 predicted fragment length is 66 bps INFO @ Sat, 03 Apr 2021 10:03:03: #2 alternative fragment length(s) may be 4,66 bps INFO @ Sat, 03 Apr 2021 10:03:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.10_model.r WARNING @ Sat, 03 Apr 2021 10:03:03: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:03:03: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Sat, 03 Apr 2021 10:03:03: #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 10:03:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:03:03: #1 tags after filtering in treatment: 8632249 INFO @ Sat, 03 Apr 2021 10:03:03: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 10:03:03: #1 finished! INFO @ Sat, 03 Apr 2021 10:03:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:03:04: #2 number of paired peaks: 522 WARNING @ Sat, 03 Apr 2021 10:03:04: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sat, 03 Apr 2021 10:03:04: start model_add_line... INFO @ Sat, 03 Apr 2021 10:03:04: start X-correlation... INFO @ Sat, 03 Apr 2021 10:03:04: end of X-cor INFO @ Sat, 03 Apr 2021 10:03:04: #2 finished! INFO @ Sat, 03 Apr 2021 10:03:04: #2 predicted fragment length is 66 bps INFO @ Sat, 03 Apr 2021 10:03:04: #2 alternative fragment length(s) may be 4,66 bps INFO @ Sat, 03 Apr 2021 10:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.20_model.r WARNING @ Sat, 03 Apr 2021 10:03:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:03:04: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Sat, 03 Apr 2021 10:03:04: #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 10:03:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:03:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:03:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.10_peaks.xls INFO @ Sat, 03 Apr 2021 10:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.20_peaks.xls INFO @ Sat, 03 Apr 2021 10:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.20_summits.bed INFO @ Sat, 03 Apr 2021 10:03:39: Done! INFO @ Sat, 03 Apr 2021 10:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174041/SRX8174041.10_summits.bed INFO @ Sat, 03 Apr 2021 10:03:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1682 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。