Job ID = 14171794 SRX = SRX9008839 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15083077 spots for SRR12518311/SRR12518311.sra Written 15083077 spots for SRR12518311/SRR12518311.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172341 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:29:26 15083077 reads; of these: 15083077 (100.00%) were paired; of these: 2827629 (18.75%) aligned concordantly 0 times 10026230 (66.47%) aligned concordantly exactly 1 time 2229218 (14.78%) aligned concordantly >1 times ---- 2827629 pairs aligned concordantly 0 times; of these: 1540449 (54.48%) aligned discordantly 1 time ---- 1287180 pairs aligned 0 times concordantly or discordantly; of these: 2574360 mates make up the pairs; of these: 1690585 (65.67%) aligned 0 times 311342 (12.09%) aligned exactly 1 time 572433 (22.24%) aligned >1 times 94.40% overall alignment rate Time searching: 00:29:27 Overall time: 00:29:27 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] 708088 / 13654017 = 0.0519 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 13:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.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 13:31:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:31:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:31:15: 1000000 INFO @ Sat, 11 Dec 2021 13:31:22: 2000000 INFO @ Sat, 11 Dec 2021 13:31:29: 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 13:31:36: 4000000 INFO @ Sat, 11 Dec 2021 13:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.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 13:31:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:31:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:31:44: 5000000 INFO @ Sat, 11 Dec 2021 13:31:46: 1000000 INFO @ Sat, 11 Dec 2021 13:31:53: 6000000 INFO @ Sat, 11 Dec 2021 13:31:54: 2000000 INFO @ Sat, 11 Dec 2021 13:32:01: 7000000 INFO @ Sat, 11 Dec 2021 13:32:03: 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 @ Sat, 11 Dec 2021 13:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.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 13:32:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:09: 8000000 INFO @ Sat, 11 Dec 2021 13:32:11: 4000000 INFO @ Sat, 11 Dec 2021 13:32:16: 1000000 INFO @ Sat, 11 Dec 2021 13:32:18: 9000000 INFO @ Sat, 11 Dec 2021 13:32:20: 5000000 INFO @ Sat, 11 Dec 2021 13:32:24: 2000000 INFO @ Sat, 11 Dec 2021 13:32:26: 10000000 INFO @ Sat, 11 Dec 2021 13:32:28: 6000000 INFO @ Sat, 11 Dec 2021 13:32:33: 3000000 INFO @ Sat, 11 Dec 2021 13:32:35: 11000000 INFO @ Sat, 11 Dec 2021 13:32:37: 7000000 INFO @ Sat, 11 Dec 2021 13:32:41: 4000000 INFO @ Sat, 11 Dec 2021 13:32:43: 12000000 INFO @ Sat, 11 Dec 2021 13:32:45: 8000000 INFO @ Sat, 11 Dec 2021 13:32:50: 5000000 INFO @ Sat, 11 Dec 2021 13:32:51: 13000000 INFO @ Sat, 11 Dec 2021 13:32:54: 9000000 INFO @ Sat, 11 Dec 2021 13:32:58: 6000000 INFO @ Sat, 11 Dec 2021 13:33:00: 14000000 INFO @ Sat, 11 Dec 2021 13:33:02: 10000000 INFO @ Sat, 11 Dec 2021 13:33:06: 7000000 INFO @ Sat, 11 Dec 2021 13:33:08: 15000000 INFO @ Sat, 11 Dec 2021 13:33:11: 11000000 INFO @ Sat, 11 Dec 2021 13:33:15: 8000000 INFO @ Sat, 11 Dec 2021 13:33:16: 16000000 INFO @ Sat, 11 Dec 2021 13:33:19: 12000000 INFO @ Sat, 11 Dec 2021 13:33:23: 9000000 INFO @ Sat, 11 Dec 2021 13:33:25: 17000000 INFO @ Sat, 11 Dec 2021 13:33:27: 13000000 INFO @ Sat, 11 Dec 2021 13:33:31: 10000000 INFO @ Sat, 11 Dec 2021 13:33:33: 18000000 INFO @ Sat, 11 Dec 2021 13:33:36: 14000000 INFO @ Sat, 11 Dec 2021 13:33:40: 11000000 INFO @ Sat, 11 Dec 2021 13:33:41: 19000000 INFO @ Sat, 11 Dec 2021 13:33:44: 15000000 INFO @ Sat, 11 Dec 2021 13:33:48: 12000000 INFO @ Sat, 11 Dec 2021 13:33:50: 20000000 INFO @ Sat, 11 Dec 2021 13:33:52: 16000000 INFO @ Sat, 11 Dec 2021 13:33:56: 13000000 INFO @ Sat, 11 Dec 2021 13:33:58: 21000000 INFO @ Sat, 11 Dec 2021 13:34:01: 17000000 INFO @ Sat, 11 Dec 2021 13:34:05: 14000000 INFO @ Sat, 11 Dec 2021 13:34:06: 22000000 INFO @ Sat, 11 Dec 2021 13:34:09: 18000000 INFO @ Sat, 11 Dec 2021 13:34:13: 15000000 INFO @ Sat, 11 Dec 2021 13:34:15: 23000000 INFO @ Sat, 11 Dec 2021 13:34:17: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:34:21: 16000000 INFO @ Sat, 11 Dec 2021 13:34:23: 24000000 INFO @ Sat, 11 Dec 2021 13:34:25: 20000000 INFO @ Sat, 11 Dec 2021 13:34:29: 17000000 INFO @ Sat, 11 Dec 2021 13:34:31: 25000000 INFO @ Sat, 11 Dec 2021 13:34:34: 21000000 INFO @ Sat, 11 Dec 2021 13:34:38: 18000000 INFO @ Sat, 11 Dec 2021 13:34:40: 26000000 INFO @ Sat, 11 Dec 2021 13:34:42: 22000000 INFO @ Sat, 11 Dec 2021 13:34:46: 19000000 INFO @ Sat, 11 Dec 2021 13:34:48: 27000000 INFO @ Sat, 11 Dec 2021 13:34:49: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:34:49: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:34:49: #1 total tags in treatment: 11606390 INFO @ Sat, 11 Dec 2021 13:34:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:34:49: #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 13:34:49: #1 tags after filtering in treatment: 11193892 INFO @ Sat, 11 Dec 2021 13:34:49: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:34:49: #1 finished! INFO @ Sat, 11 Dec 2021 13:34:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:34:50: #2 number of paired peaks: 192 WARNING @ Sat, 11 Dec 2021 13:34:50: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 11 Dec 2021 13:34:50: start model_add_line... INFO @ Sat, 11 Dec 2021 13:34:50: start X-correlation... INFO @ Sat, 11 Dec 2021 13:34:50: end of X-cor INFO @ Sat, 11 Dec 2021 13:34:50: #2 finished! INFO @ Sat, 11 Dec 2021 13:34:50: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 13:34:50: #2 alternative fragment length(s) may be 2,168,515,537,578 bps INFO @ Sat, 11 Dec 2021 13:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.05_model.r WARNING @ Sat, 11 Dec 2021 13:34:50: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:34:50: #2 You may need to consider one of the other alternative d(s): 2,168,515,537,578 WARNING @ Sat, 11 Dec 2021 13:34:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:34:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:34:50: 23000000 INFO @ Sat, 11 Dec 2021 13:34:54: 20000000 INFO @ Sat, 11 Dec 2021 13:34:59: 24000000 INFO @ Sat, 11 Dec 2021 13:35:03: 21000000 INFO @ Sat, 11 Dec 2021 13:35:07: 25000000 INFO @ Sat, 11 Dec 2021 13:35:11: 22000000 INFO @ Sat, 11 Dec 2021 13:35:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:35:15: 26000000 INFO @ Sat, 11 Dec 2021 13:35:19: 23000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:35:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:35:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:35:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.05_summits.bed INFO @ Sat, 11 Dec 2021 13:35:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:35:23: 27000000 INFO @ Sat, 11 Dec 2021 13:35:24: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:35:24: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:35:24: #1 total tags in treatment: 11606390 INFO @ Sat, 11 Dec 2021 13:35:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:35:24: #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 13:35:24: #1 tags after filtering in treatment: 11193892 INFO @ Sat, 11 Dec 2021 13:35:24: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:35:24: #1 finished! INFO @ Sat, 11 Dec 2021 13:35:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:35:25: #2 number of paired peaks: 192 WARNING @ Sat, 11 Dec 2021 13:35:25: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 11 Dec 2021 13:35:25: start model_add_line... INFO @ Sat, 11 Dec 2021 13:35:25: start X-correlation... INFO @ Sat, 11 Dec 2021 13:35:25: end of X-cor INFO @ Sat, 11 Dec 2021 13:35:25: #2 finished! INFO @ Sat, 11 Dec 2021 13:35:25: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 13:35:25: #2 alternative fragment length(s) may be 2,168,515,537,578 bps INFO @ Sat, 11 Dec 2021 13:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.10_model.r WARNING @ Sat, 11 Dec 2021 13:35:25: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:35:25: #2 You may need to consider one of the other alternative d(s): 2,168,515,537,578 WARNING @ Sat, 11 Dec 2021 13:35:25: #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 13:35:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:35:27: 24000000 INFO @ Sat, 11 Dec 2021 13:35:35: 25000000 INFO @ Sat, 11 Dec 2021 13:35:42: 26000000 INFO @ Sat, 11 Dec 2021 13:35:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:35:49: 27000000 INFO @ Sat, 11 Dec 2021 13:35:49: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:35:49: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:35:49: #1 total tags in treatment: 11606390 INFO @ Sat, 11 Dec 2021 13:35:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:35:49: #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 13:35:49: #1 tags after filtering in treatment: 11193892 INFO @ Sat, 11 Dec 2021 13:35:49: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:35:49: #1 finished! INFO @ Sat, 11 Dec 2021 13:35:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:35:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:35:50: #2 number of paired peaks: 192 WARNING @ Sat, 11 Dec 2021 13:35:50: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 11 Dec 2021 13:35:50: start model_add_line... INFO @ Sat, 11 Dec 2021 13:35:50: start X-correlation... INFO @ Sat, 11 Dec 2021 13:35:50: end of X-cor INFO @ Sat, 11 Dec 2021 13:35:50: #2 finished! INFO @ Sat, 11 Dec 2021 13:35:50: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 13:35:50: #2 alternative fragment length(s) may be 2,168,515,537,578 bps INFO @ Sat, 11 Dec 2021 13:35:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.20_model.r WARNING @ Sat, 11 Dec 2021 13:35:50: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:35:50: #2 You may need to consider one of the other alternative d(s): 2,168,515,537,578 WARNING @ Sat, 11 Dec 2021 13:35:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:35:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:35:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.10_summits.bed INFO @ Sat, 11 Dec 2021 13:35:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:36:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008839/SRX9008839.20_summits.bed INFO @ Sat, 11 Dec 2021 13:36:23: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 1 millis CompletedMACS2peakCalling