Job ID = 14167103 SRX = SRX10412065 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17365060 spots for SRR14035700/SRR14035700.sra Written 17365060 spots for SRR14035700/SRR14035700.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167897 ("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: 01:40:22 17365060 reads; of these: 17365060 (100.00%) were paired; of these: 2083154 (12.00%) aligned concordantly 0 times 11113164 (64.00%) aligned concordantly exactly 1 time 4168742 (24.01%) aligned concordantly >1 times ---- 2083154 pairs aligned concordantly 0 times; of these: 321697 (15.44%) aligned discordantly 1 time ---- 1761457 pairs aligned 0 times concordantly or discordantly; of these: 3522914 mates make up the pairs; of these: 2725750 (77.37%) aligned 0 times 296932 (8.43%) aligned exactly 1 time 500232 (14.20%) aligned >1 times 92.15% overall alignment rate Time searching: 01:40:22 Overall time: 01:40:22 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 24 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] 3507455 / 15570974 = 0.2253 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 11:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.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 11:54:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:54:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:54:52: 1000000 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 11:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.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 11:55:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:55:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:55:10: 2000000 INFO @ Fri, 10 Dec 2021 11:55:23: 1000000 INFO @ Fri, 10 Dec 2021 11:55:29: 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 11:55:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.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 11:55:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:55:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:55:44: 2000000 INFO @ Fri, 10 Dec 2021 11:55:49: 4000000 INFO @ Fri, 10 Dec 2021 11:55:50: 1000000 INFO @ Fri, 10 Dec 2021 11:56:06: 3000000 INFO @ Fri, 10 Dec 2021 11:56:06: 2000000 INFO @ Fri, 10 Dec 2021 11:56:10: 5000000 INFO @ Fri, 10 Dec 2021 11:56:23: 3000000 INFO @ Fri, 10 Dec 2021 11:56:27: 4000000 INFO @ Fri, 10 Dec 2021 11:56:29: 6000000 INFO @ Fri, 10 Dec 2021 11:56:39: 4000000 INFO @ Fri, 10 Dec 2021 11:56:48: 5000000 INFO @ Fri, 10 Dec 2021 11:56:50: 7000000 INFO @ Fri, 10 Dec 2021 11:56:55: 5000000 INFO @ Fri, 10 Dec 2021 11:57:10: 6000000 INFO @ Fri, 10 Dec 2021 11:57:12: 8000000 INFO @ Fri, 10 Dec 2021 11:57:13: 6000000 INFO @ Fri, 10 Dec 2021 11:57:31: 7000000 INFO @ Fri, 10 Dec 2021 11:57:31: 7000000 INFO @ Fri, 10 Dec 2021 11:57:34: 9000000 INFO @ Fri, 10 Dec 2021 11:57:49: 8000000 INFO @ Fri, 10 Dec 2021 11:57:55: 8000000 INFO @ Fri, 10 Dec 2021 11:57:58: 10000000 INFO @ Fri, 10 Dec 2021 11:58:06: 9000000 INFO @ Fri, 10 Dec 2021 11:58:18: 9000000 INFO @ Fri, 10 Dec 2021 11:58:22: 11000000 INFO @ Fri, 10 Dec 2021 11:58:23: 10000000 INFO @ Fri, 10 Dec 2021 11:58:40: 11000000 INFO @ Fri, 10 Dec 2021 11:58:41: 10000000 INFO @ Fri, 10 Dec 2021 11:58:46: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:58:57: 12000000 INFO @ Fri, 10 Dec 2021 11:59:04: 11000000 INFO @ Fri, 10 Dec 2021 11:59:10: 13000000 INFO @ Fri, 10 Dec 2021 11:59:14: 13000000 INFO @ Fri, 10 Dec 2021 11:59:27: 12000000 INFO @ Fri, 10 Dec 2021 11:59:31: 14000000 INFO @ Fri, 10 Dec 2021 11:59:34: 14000000 INFO @ Fri, 10 Dec 2021 11:59:48: 13000000 INFO @ Fri, 10 Dec 2021 11:59:49: 15000000 INFO @ Fri, 10 Dec 2021 11:59:58: 15000000 INFO @ Fri, 10 Dec 2021 12:00:06: 16000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:00:11: 14000000 INFO @ Fri, 10 Dec 2021 12:00:21: 16000000 INFO @ Fri, 10 Dec 2021 12:00:23: 17000000 INFO @ Fri, 10 Dec 2021 12:00:33: 15000000 INFO @ Fri, 10 Dec 2021 12:00:40: 18000000 INFO @ Fri, 10 Dec 2021 12:00:42: 17000000 INFO @ Fri, 10 Dec 2021 12:00:55: 16000000 INFO @ Fri, 10 Dec 2021 12:00:57: 19000000 INFO @ Fri, 10 Dec 2021 12:01:03: 18000000 INFO @ Fri, 10 Dec 2021 12:01:13: 20000000 INFO @ Fri, 10 Dec 2021 12:01:18: 17000000 INFO @ Fri, 10 Dec 2021 12:01:25: 19000000 INFO @ Fri, 10 Dec 2021 12:01:30: 21000000 INFO @ Fri, 10 Dec 2021 12:01:40: 18000000 INFO @ Fri, 10 Dec 2021 12:01:46: 20000000 INFO @ Fri, 10 Dec 2021 12:01:47: 22000000 INFO @ Fri, 10 Dec 2021 12:02:03: 19000000 INFO @ Fri, 10 Dec 2021 12:02:03: 23000000 INFO @ Fri, 10 Dec 2021 12:02:07: 21000000 INFO @ Fri, 10 Dec 2021 12:02:19: 24000000 INFO @ Fri, 10 Dec 2021 12:02:26: 20000000 INFO @ Fri, 10 Dec 2021 12:02:28: 22000000 INFO @ Fri, 10 Dec 2021 12:02:35: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 12:02:35: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 12:02:35: #1 total tags in treatment: 11828825 INFO @ Fri, 10 Dec 2021 12:02:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:02:35: #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 12:02:35: #1 tags after filtering in treatment: 11067680 INFO @ Fri, 10 Dec 2021 12:02:35: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 12:02:35: #1 finished! INFO @ Fri, 10 Dec 2021 12:02:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:02:36: #2 number of paired peaks: 375 WARNING @ Fri, 10 Dec 2021 12:02:36: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Fri, 10 Dec 2021 12:02:36: start model_add_line... INFO @ Fri, 10 Dec 2021 12:02:36: start X-correlation... INFO @ Fri, 10 Dec 2021 12:02:36: end of X-cor INFO @ Fri, 10 Dec 2021 12:02:36: #2 finished! INFO @ Fri, 10 Dec 2021 12:02:36: #2 predicted fragment length is 200 bps INFO @ Fri, 10 Dec 2021 12:02:36: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 10 Dec 2021 12:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.20_model.r WARNING @ Fri, 10 Dec 2021 12:02:36: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:02:36: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Fri, 10 Dec 2021 12:02:36: #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 12:02:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:02:48: 21000000 INFO @ Fri, 10 Dec 2021 12:02:49: 23000000 INFO @ Fri, 10 Dec 2021 12:03:09: 22000000 INFO @ Fri, 10 Dec 2021 12:03:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:03:09: 24000000 INFO @ Fri, 10 Dec 2021 12:03:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:03:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:03:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.20_summits.bed INFO @ Fri, 10 Dec 2021 12:03:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1552 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:03:30: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 12:03:30: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 12:03:30: #1 total tags in treatment: 11828825 INFO @ Fri, 10 Dec 2021 12:03:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:03:30: #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 12:03:30: #1 tags after filtering in treatment: 11067680 INFO @ Fri, 10 Dec 2021 12:03:30: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 12:03:30: #1 finished! INFO @ Fri, 10 Dec 2021 12:03:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:03:31: #2 number of paired peaks: 375 WARNING @ Fri, 10 Dec 2021 12:03:31: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Fri, 10 Dec 2021 12:03:31: start model_add_line... INFO @ Fri, 10 Dec 2021 12:03:31: start X-correlation... INFO @ Fri, 10 Dec 2021 12:03:31: end of X-cor INFO @ Fri, 10 Dec 2021 12:03:31: #2 finished! INFO @ Fri, 10 Dec 2021 12:03:31: #2 predicted fragment length is 200 bps INFO @ Fri, 10 Dec 2021 12:03:31: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 10 Dec 2021 12:03:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.05_model.r WARNING @ Fri, 10 Dec 2021 12:03:31: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:03:31: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Fri, 10 Dec 2021 12:03:31: #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 12:03:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:03:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:03:31: 23000000 INFO @ Fri, 10 Dec 2021 12:03:50: 24000000 INFO @ Fri, 10 Dec 2021 12:04:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:04:10: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 12:04:10: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 12:04:10: #1 total tags in treatment: 11828825 INFO @ Fri, 10 Dec 2021 12:04:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:04:10: #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 12:04:10: #1 tags after filtering in treatment: 11067680 INFO @ Fri, 10 Dec 2021 12:04:10: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 12:04:10: #1 finished! INFO @ Fri, 10 Dec 2021 12:04:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:04:11: #2 number of paired peaks: 375 WARNING @ Fri, 10 Dec 2021 12:04:11: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Fri, 10 Dec 2021 12:04:11: start model_add_line... INFO @ Fri, 10 Dec 2021 12:04:11: start X-correlation... INFO @ Fri, 10 Dec 2021 12:04:11: end of X-cor INFO @ Fri, 10 Dec 2021 12:04:11: #2 finished! INFO @ Fri, 10 Dec 2021 12:04:11: #2 predicted fragment length is 200 bps INFO @ Fri, 10 Dec 2021 12:04:11: #2 alternative fragment length(s) may be 200 bps INFO @ Fri, 10 Dec 2021 12:04:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.10_model.r WARNING @ Fri, 10 Dec 2021 12:04:11: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:04:11: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Fri, 10 Dec 2021 12:04:11: #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 12:04:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:04:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:04:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:04:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:04:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.05_summits.bed INFO @ Fri, 10 Dec 2021 12:04:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8133 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:04:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:05:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:05:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:05:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412065/SRX10412065.10_summits.bed INFO @ Fri, 10 Dec 2021 12:05:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4555 records, 4 fields): 8 millis CompletedMACS2peakCalling