Job ID = 14167201 SRX = SRX8913806 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23695479 spots for SRR12417805/SRR12417805.sra Written 23695479 spots for SRR12417805/SRR12417805.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168335 ("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: 02:33:34 23695479 reads; of these: 23695479 (100.00%) were paired; of these: 11708748 (49.41%) aligned concordantly 0 times 5408465 (22.82%) aligned concordantly exactly 1 time 6578266 (27.76%) aligned concordantly >1 times ---- 11708748 pairs aligned concordantly 0 times; of these: 3390379 (28.96%) aligned discordantly 1 time ---- 8318369 pairs aligned 0 times concordantly or discordantly; of these: 16636738 mates make up the pairs; of these: 12952999 (77.86%) aligned 0 times 740579 (4.45%) aligned exactly 1 time 2943160 (17.69%) aligned >1 times 72.67% overall alignment rate Time searching: 02:33:35 Overall time: 02:33:35 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 28 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] 3291781 / 15055836 = 0.2186 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 13:49:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.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 13:49:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:49:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:49:45: 1000000 INFO @ Fri, 10 Dec 2021 13:49:52: 2000000 INFO @ Fri, 10 Dec 2021 13:50:00: 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 13:50:07: 4000000 INFO @ Fri, 10 Dec 2021 13:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.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 13:50:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:50:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:50:15: 5000000 INFO @ Fri, 10 Dec 2021 13:50:15: 1000000 INFO @ Fri, 10 Dec 2021 13:50:23: 6000000 INFO @ Fri, 10 Dec 2021 13:50:24: 2000000 INFO @ Fri, 10 Dec 2021 13:50:30: 7000000 INFO @ Fri, 10 Dec 2021 13:50:32: 3000000 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 13:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.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 13:50:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:50:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:50:38: 8000000 INFO @ Fri, 10 Dec 2021 13:50:40: 4000000 INFO @ Fri, 10 Dec 2021 13:50:44: 1000000 INFO @ Fri, 10 Dec 2021 13:50:46: 9000000 INFO @ Fri, 10 Dec 2021 13:50:48: 5000000 INFO @ Fri, 10 Dec 2021 13:50:50: 2000000 INFO @ Fri, 10 Dec 2021 13:50:54: 10000000 INFO @ Fri, 10 Dec 2021 13:50:56: 6000000 INFO @ Fri, 10 Dec 2021 13:50:56: 3000000 INFO @ Fri, 10 Dec 2021 13:51:02: 11000000 INFO @ Fri, 10 Dec 2021 13:51:03: 4000000 INFO @ Fri, 10 Dec 2021 13:51:04: 7000000 INFO @ Fri, 10 Dec 2021 13:51:09: 5000000 INFO @ Fri, 10 Dec 2021 13:51:09: 12000000 INFO @ Fri, 10 Dec 2021 13:51:12: 8000000 INFO @ Fri, 10 Dec 2021 13:51:16: 6000000 INFO @ Fri, 10 Dec 2021 13:51:17: 13000000 INFO @ Fri, 10 Dec 2021 13:51:20: 9000000 INFO @ Fri, 10 Dec 2021 13:51:22: 7000000 INFO @ Fri, 10 Dec 2021 13:51:25: 14000000 INFO @ Fri, 10 Dec 2021 13:51:28: 8000000 INFO @ Fri, 10 Dec 2021 13:51:29: 10000000 INFO @ Fri, 10 Dec 2021 13:51:33: 15000000 INFO @ Fri, 10 Dec 2021 13:51:35: 9000000 INFO @ Fri, 10 Dec 2021 13:51:37: 11000000 INFO @ Fri, 10 Dec 2021 13:51:40: 16000000 INFO @ Fri, 10 Dec 2021 13:51:41: 10000000 INFO @ Fri, 10 Dec 2021 13:51:45: 12000000 INFO @ Fri, 10 Dec 2021 13:51:47: 11000000 INFO @ Fri, 10 Dec 2021 13:51:48: 17000000 INFO @ Fri, 10 Dec 2021 13:51:53: 13000000 INFO @ Fri, 10 Dec 2021 13:51:54: 12000000 INFO @ Fri, 10 Dec 2021 13:51:56: 18000000 INFO @ Fri, 10 Dec 2021 13:52:00: 13000000 INFO @ Fri, 10 Dec 2021 13:52:02: 14000000 INFO @ Fri, 10 Dec 2021 13:52:04: 19000000 INFO @ Fri, 10 Dec 2021 13:52:06: 14000000 INFO @ Fri, 10 Dec 2021 13:52:10: 15000000 INFO @ Fri, 10 Dec 2021 13:52:12: 20000000 INFO @ Fri, 10 Dec 2021 13:52:13: 15000000 INFO @ Fri, 10 Dec 2021 13:52:18: 16000000 INFO @ Fri, 10 Dec 2021 13:52:19: 16000000 INFO @ Fri, 10 Dec 2021 13:52:19: 21000000 INFO @ Fri, 10 Dec 2021 13:52:26: 17000000 INFO @ Fri, 10 Dec 2021 13:52:27: 17000000 INFO @ Fri, 10 Dec 2021 13:52:27: 22000000 INFO @ Fri, 10 Dec 2021 13:52:35: 18000000 INFO @ Fri, 10 Dec 2021 13:52:35: 18000000 INFO @ Fri, 10 Dec 2021 13:52:35: 23000000 INFO @ Fri, 10 Dec 2021 13:52:43: 19000000 INFO @ Fri, 10 Dec 2021 13:52:43: 24000000 INFO @ Fri, 10 Dec 2021 13:52:43: 19000000 INFO @ Fri, 10 Dec 2021 13:52:51: 20000000 INFO @ Fri, 10 Dec 2021 13:52:51: 25000000 INFO @ Fri, 10 Dec 2021 13:52:51: 20000000 INFO @ Fri, 10 Dec 2021 13:52:59: 21000000 INFO @ Fri, 10 Dec 2021 13:53:00: 21000000 INFO @ Fri, 10 Dec 2021 13:53:00: 26000000 INFO @ Fri, 10 Dec 2021 13:53:07: 22000000 INFO @ Fri, 10 Dec 2021 13:53:08: 27000000 INFO @ Fri, 10 Dec 2021 13:53:08: 22000000 INFO @ Fri, 10 Dec 2021 13:53:15: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 13:53:15: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 13:53:15: #1 total tags in treatment: 9009011 INFO @ Fri, 10 Dec 2021 13:53:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:53:15: #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 13:53:15: #1 tags after filtering in treatment: 6831068 INFO @ Fri, 10 Dec 2021 13:53:15: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Dec 2021 13:53:15: #1 finished! INFO @ Fri, 10 Dec 2021 13:53:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:53:15: #2 number of paired peaks: 907 WARNING @ Fri, 10 Dec 2021 13:53:15: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Fri, 10 Dec 2021 13:53:15: start model_add_line... INFO @ Fri, 10 Dec 2021 13:53:15: start X-correlation... INFO @ Fri, 10 Dec 2021 13:53:15: end of X-cor INFO @ Fri, 10 Dec 2021 13:53:15: #2 finished! INFO @ Fri, 10 Dec 2021 13:53:15: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 13:53:15: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 13:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.05_model.r WARNING @ Fri, 10 Dec 2021 13:53:15: #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 13:53:15: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 10 Dec 2021 13:53:15: #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 13:53:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:53:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:53:16: 23000000 INFO @ Fri, 10 Dec 2021 13:53:16: 23000000 INFO @ Fri, 10 Dec 2021 13:53:24: 24000000 INFO @ Fri, 10 Dec 2021 13:53:24: 24000000 INFO @ Fri, 10 Dec 2021 13:53:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:53:32: 25000000 INFO @ Fri, 10 Dec 2021 13:53:33: 25000000 INFO @ Fri, 10 Dec 2021 13:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.05_summits.bed INFO @ Fri, 10 Dec 2021 13:53:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2804 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:53:41: 26000000 INFO @ Fri, 10 Dec 2021 13:53:41: 26000000 INFO @ Fri, 10 Dec 2021 13:53:49: 27000000 INFO @ Fri, 10 Dec 2021 13:53:49: 27000000 INFO @ Fri, 10 Dec 2021 13:53:56: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 13:53:56: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 13:53:56: #1 total tags in treatment: 9009011 INFO @ Fri, 10 Dec 2021 13:53:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:53:56: #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 13:53:56: #1 tags after filtering in treatment: 6831068 INFO @ Fri, 10 Dec 2021 13:53:56: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Dec 2021 13:53:56: #1 finished! INFO @ Fri, 10 Dec 2021 13:53:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:53:56: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 13:53:56: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 13:53:56: #1 total tags in treatment: 9009011 INFO @ Fri, 10 Dec 2021 13:53:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:53:56: #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 13:53:56: #1 tags after filtering in treatment: 6831068 INFO @ Fri, 10 Dec 2021 13:53:56: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Dec 2021 13:53:56: #1 finished! INFO @ Fri, 10 Dec 2021 13:53:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:53:56: #2 number of paired peaks: 907 WARNING @ Fri, 10 Dec 2021 13:53:56: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Fri, 10 Dec 2021 13:53:56: start model_add_line... INFO @ Fri, 10 Dec 2021 13:53:56: start X-correlation... INFO @ Fri, 10 Dec 2021 13:53:56: end of X-cor INFO @ Fri, 10 Dec 2021 13:53:56: #2 finished! INFO @ Fri, 10 Dec 2021 13:53:56: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 13:53:56: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 13:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.10_model.r WARNING @ Fri, 10 Dec 2021 13:53:56: #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 13:53:56: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 10 Dec 2021 13:53:56: #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 13:53:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:53:57: #2 number of paired peaks: 907 WARNING @ Fri, 10 Dec 2021 13:53:57: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Fri, 10 Dec 2021 13:53:57: start model_add_line... INFO @ Fri, 10 Dec 2021 13:53:57: start X-correlation... INFO @ Fri, 10 Dec 2021 13:53:57: end of X-cor INFO @ Fri, 10 Dec 2021 13:53:57: #2 finished! INFO @ Fri, 10 Dec 2021 13:53:57: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 13:53:57: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 13:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.20_model.r WARNING @ Fri, 10 Dec 2021 13:53:57: #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 13:53:57: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Fri, 10 Dec 2021 13:53:57: #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 13:53:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:53:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:54:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:54:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.20_summits.bed INFO @ Fri, 10 Dec 2021 13:54:19: Done! INFO @ Fri, 10 Dec 2021 13:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913806/SRX8913806.10_summits.bed INFO @ Fri, 10 Dec 2021 13:54:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1059 records, 4 fields): 3 millis pass1 - making usageList (15 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (1599 records, 4 fields): 3 millis CompletedMACS2peakCalling