Job ID = 12266667 SRX = SRX7806734 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14926168 spots for SRR11186400/SRR11186400.sra Written 14926168 spots for SRR11186400/SRR11186400.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266931 ("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: 00:16:44 14926168 reads; of these: 14926168 (100.00%) were paired; of these: 9204375 (61.67%) aligned concordantly 0 times 3758832 (25.18%) aligned concordantly exactly 1 time 1962961 (13.15%) aligned concordantly >1 times ---- 9204375 pairs aligned concordantly 0 times; of these: 809540 (8.80%) aligned discordantly 1 time ---- 8394835 pairs aligned 0 times concordantly or discordantly; of these: 16789670 mates make up the pairs; of these: 15681282 (93.40%) aligned 0 times 425249 (2.53%) aligned exactly 1 time 683139 (4.07%) aligned >1 times 47.47% overall alignment rate Time searching: 00:16:44 Overall time: 00:16:44 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 8 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] 1193819 / 6486729 = 0.1840 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 09:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.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 09:26:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:26:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:26:56: 1000000 INFO @ Sat, 03 Apr 2021 09:27:02: 2000000 INFO @ Sat, 03 Apr 2021 09:27:09: 3000000 INFO @ Sat, 03 Apr 2021 09:27:15: 4000000 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 09:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.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 09:27:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:27:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:27:21: 5000000 INFO @ Sat, 03 Apr 2021 09:27:27: 1000000 INFO @ Sat, 03 Apr 2021 09:27:29: 6000000 INFO @ Sat, 03 Apr 2021 09:27:34: 2000000 INFO @ Sat, 03 Apr 2021 09:27:36: 7000000 INFO @ Sat, 03 Apr 2021 09:27:42: 3000000 INFO @ Sat, 03 Apr 2021 09:27:44: 8000000 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 09:27:49: 4000000 INFO @ Sat, 03 Apr 2021 09:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.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 09:27:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:27:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:27:51: 9000000 INFO @ Sat, 03 Apr 2021 09:27:57: 5000000 INFO @ Sat, 03 Apr 2021 09:27:57: 1000000 INFO @ Sat, 03 Apr 2021 09:27:58: 10000000 INFO @ Sat, 03 Apr 2021 09:28:04: 6000000 INFO @ Sat, 03 Apr 2021 09:28:04: 2000000 INFO @ Sat, 03 Apr 2021 09:28:06: 11000000 INFO @ Sat, 03 Apr 2021 09:28:12: 7000000 INFO @ Sat, 03 Apr 2021 09:28:12: 3000000 INFO @ Sat, 03 Apr 2021 09:28:12: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:28:12: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:28:12: #1 total tags in treatment: 4605490 INFO @ Sat, 03 Apr 2021 09:28:12: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:28:12: #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 09:28:12: #1 tags after filtering in treatment: 3930023 INFO @ Sat, 03 Apr 2021 09:28:12: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 09:28:12: #1 finished! INFO @ Sat, 03 Apr 2021 09:28:12: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:28:12: #2 number of paired peaks: 500 WARNING @ Sat, 03 Apr 2021 09:28:12: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Sat, 03 Apr 2021 09:28:12: start model_add_line... INFO @ Sat, 03 Apr 2021 09:28:12: start X-correlation... INFO @ Sat, 03 Apr 2021 09:28:12: end of X-cor INFO @ Sat, 03 Apr 2021 09:28:12: #2 finished! INFO @ Sat, 03 Apr 2021 09:28:12: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 09:28:12: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 09:28:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.05_model.r WARNING @ Sat, 03 Apr 2021 09:28:12: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:28:12: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sat, 03 Apr 2021 09:28:12: #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 09:28:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:28:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:28:19: 8000000 INFO @ Sat, 03 Apr 2021 09:28:19: 4000000 INFO @ Sat, 03 Apr 2021 09:28:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.05_summits.bed INFO @ Sat, 03 Apr 2021 09:28:26: Done! INFO @ Sat, 03 Apr 2021 09:28:26: 9000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2168 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:28:27: 5000000 INFO @ Sat, 03 Apr 2021 09:28:34: 10000000 INFO @ Sat, 03 Apr 2021 09:28:34: 6000000 INFO @ Sat, 03 Apr 2021 09:28:41: 7000000 INFO @ Sat, 03 Apr 2021 09:28:41: 11000000 INFO @ Sat, 03 Apr 2021 09:28:47: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:28:47: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:28:47: #1 total tags in treatment: 4605490 INFO @ Sat, 03 Apr 2021 09:28:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:28:47: #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 09:28:47: #1 tags after filtering in treatment: 3930023 INFO @ Sat, 03 Apr 2021 09:28:47: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 09:28:47: #1 finished! INFO @ Sat, 03 Apr 2021 09:28:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:28:47: #2 number of paired peaks: 500 WARNING @ Sat, 03 Apr 2021 09:28:47: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Sat, 03 Apr 2021 09:28:47: start model_add_line... INFO @ Sat, 03 Apr 2021 09:28:47: start X-correlation... INFO @ Sat, 03 Apr 2021 09:28:47: end of X-cor INFO @ Sat, 03 Apr 2021 09:28:47: #2 finished! INFO @ Sat, 03 Apr 2021 09:28:47: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 09:28:47: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 09:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.10_model.r WARNING @ Sat, 03 Apr 2021 09:28:47: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:28:47: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sat, 03 Apr 2021 09:28:47: #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 09:28:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:28:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:28:48: 8000000 INFO @ Sat, 03 Apr 2021 09:28:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:28:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:29:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.10_summits.bed INFO @ Sat, 03 Apr 2021 09:29:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (845 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:29:02: 10000000 INFO @ Sat, 03 Apr 2021 09:29:09: 11000000 INFO @ Sat, 03 Apr 2021 09:29:14: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:29:14: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:29:14: #1 total tags in treatment: 4605490 INFO @ Sat, 03 Apr 2021 09:29:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:29:14: #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 09:29:14: #1 tags after filtering in treatment: 3930023 INFO @ Sat, 03 Apr 2021 09:29:14: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 09:29:14: #1 finished! INFO @ Sat, 03 Apr 2021 09:29:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:29:15: #2 number of paired peaks: 500 WARNING @ Sat, 03 Apr 2021 09:29:15: Fewer paired peaks (500) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 500 pairs to build model! INFO @ Sat, 03 Apr 2021 09:29:15: start model_add_line... INFO @ Sat, 03 Apr 2021 09:29:15: start X-correlation... INFO @ Sat, 03 Apr 2021 09:29:15: end of X-cor INFO @ Sat, 03 Apr 2021 09:29:15: #2 finished! INFO @ Sat, 03 Apr 2021 09:29:15: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 09:29:15: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 09:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.20_model.r WARNING @ Sat, 03 Apr 2021 09:29:15: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:29:15: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sat, 03 Apr 2021 09:29:15: #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 09:29:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:29:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:29:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:29:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806734/SRX7806734.20_summits.bed INFO @ Sat, 03 Apr 2021 09:29:28: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (267 records, 4 fields): 1 millis CompletedMACS2peakCalling