Job ID = 16439507 SRX = SRX9518330 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6788209 spots for SRR13070813/SRR13070813.sra Written 6788209 spots for SRR13070813/SRR13070813.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439684 ("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: 00:24:38 6788209 reads; of these: 6788209 (100.00%) were paired; of these: 544885 (8.03%) aligned concordantly 0 times 4594734 (67.69%) aligned concordantly exactly 1 time 1648590 (24.29%) aligned concordantly >1 times ---- 544885 pairs aligned concordantly 0 times; of these: 173995 (31.93%) aligned discordantly 1 time ---- 370890 pairs aligned 0 times concordantly or discordantly; of these: 741780 mates make up the pairs; of these: 471010 (63.50%) aligned 0 times 119123 (16.06%) aligned exactly 1 time 151647 (20.44%) aligned >1 times 96.53% overall alignment rate Time searching: 00:24:38 Overall time: 00:24:38 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] 104957 / 6394456 = 0.0164 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.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 @ Tue, 02 Aug 2022 15:56:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:56:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:56:44: 1000000 INFO @ Tue, 02 Aug 2022 15:56:56: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.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 @ Tue, 02 Aug 2022 15:57:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:57:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:57:10: 3000000 INFO @ Tue, 02 Aug 2022 15:57:17: 1000000 INFO @ Tue, 02 Aug 2022 15:57:23: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.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 @ Tue, 02 Aug 2022 15:57:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:57:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:57:32: 2000000 INFO @ Tue, 02 Aug 2022 15:57:37: 5000000 INFO @ Tue, 02 Aug 2022 15:57:47: 1000000 INFO @ Tue, 02 Aug 2022 15:57:48: 3000000 INFO @ Tue, 02 Aug 2022 15:57:51: 6000000 INFO @ Tue, 02 Aug 2022 15:58:02: 2000000 INFO @ Tue, 02 Aug 2022 15:58:03: 4000000 INFO @ Tue, 02 Aug 2022 15:58:05: 7000000 INFO @ Tue, 02 Aug 2022 15:58:17: 3000000 INFO @ Tue, 02 Aug 2022 15:58:19: 8000000 INFO @ Tue, 02 Aug 2022 15:58:19: 5000000 INFO @ Tue, 02 Aug 2022 15:58:31: 4000000 INFO @ Tue, 02 Aug 2022 15:58:33: 9000000 INFO @ Tue, 02 Aug 2022 15:58:34: 6000000 INFO @ Tue, 02 Aug 2022 15:58:46: 5000000 INFO @ Tue, 02 Aug 2022 15:58:47: 10000000 INFO @ Tue, 02 Aug 2022 15:58:48: 7000000 INFO @ Tue, 02 Aug 2022 15:59:00: 6000000 INFO @ Tue, 02 Aug 2022 15:59:00: 11000000 INFO @ Tue, 02 Aug 2022 15:59:03: 8000000 INFO @ Tue, 02 Aug 2022 15:59:14: 12000000 INFO @ Tue, 02 Aug 2022 15:59:15: 7000000 INFO @ Tue, 02 Aug 2022 15:59:16: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:59:27: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:59:27: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:59:27: #1 total tags in treatment: 6140079 INFO @ Tue, 02 Aug 2022 15:59:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:59:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:59:27: #1 tags after filtering in treatment: 5947514 INFO @ Tue, 02 Aug 2022 15:59:27: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:59:27: #1 finished! INFO @ Tue, 02 Aug 2022 15:59:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:59:27: #2 number of paired peaks: 142 WARNING @ Tue, 02 Aug 2022 15:59:27: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 02 Aug 2022 15:59:27: start model_add_line... INFO @ Tue, 02 Aug 2022 15:59:27: start X-correlation... INFO @ Tue, 02 Aug 2022 15:59:27: end of X-cor INFO @ Tue, 02 Aug 2022 15:59:27: #2 finished! INFO @ Tue, 02 Aug 2022 15:59:27: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 15:59:27: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 02 Aug 2022 15:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.05_model.r WARNING @ Tue, 02 Aug 2022 15:59:27: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:59:27: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Tue, 02 Aug 2022 15:59:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:59:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:59:30: 8000000 INFO @ Tue, 02 Aug 2022 15:59:32: 10000000 INFO @ Tue, 02 Aug 2022 15:59:45: 9000000 INFO @ Tue, 02 Aug 2022 15:59:46: 11000000 INFO @ Tue, 02 Aug 2022 15:59:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:59:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.05_summits.bed INFO @ Tue, 02 Aug 2022 15:59:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (793 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:00:02: 10000000 INFO @ Tue, 02 Aug 2022 16:00:02: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:00:16: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 16:00:16: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 16:00:16: #1 total tags in treatment: 6140079 INFO @ Tue, 02 Aug 2022 16:00:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:00:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:00:16: #1 tags after filtering in treatment: 5947514 INFO @ Tue, 02 Aug 2022 16:00:16: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:00:16: #1 finished! INFO @ Tue, 02 Aug 2022 16:00:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:00:17: #2 number of paired peaks: 142 WARNING @ Tue, 02 Aug 2022 16:00:17: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 02 Aug 2022 16:00:17: start model_add_line... INFO @ Tue, 02 Aug 2022 16:00:17: start X-correlation... INFO @ Tue, 02 Aug 2022 16:00:17: end of X-cor INFO @ Tue, 02 Aug 2022 16:00:17: #2 finished! INFO @ Tue, 02 Aug 2022 16:00:17: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 16:00:17: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 02 Aug 2022 16:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.10_model.r WARNING @ Tue, 02 Aug 2022 16:00:17: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:00:17: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Tue, 02 Aug 2022 16:00:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:00:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:00:17: 11000000 INFO @ Tue, 02 Aug 2022 16:00:31: 12000000 INFO @ Tue, 02 Aug 2022 16:00:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:00:43: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 16:00:43: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 16:00:43: #1 total tags in treatment: 6140079 INFO @ Tue, 02 Aug 2022 16:00:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:00:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:00:43: #1 tags after filtering in treatment: 5947514 INFO @ Tue, 02 Aug 2022 16:00:43: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:00:43: #1 finished! INFO @ Tue, 02 Aug 2022 16:00:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:00:44: #2 number of paired peaks: 142 WARNING @ Tue, 02 Aug 2022 16:00:44: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 02 Aug 2022 16:00:44: start model_add_line... INFO @ Tue, 02 Aug 2022 16:00:44: start X-correlation... INFO @ Tue, 02 Aug 2022 16:00:44: end of X-cor INFO @ Tue, 02 Aug 2022 16:00:44: #2 finished! INFO @ Tue, 02 Aug 2022 16:00:44: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 16:00:44: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 02 Aug 2022 16:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.20_model.r WARNING @ Tue, 02 Aug 2022 16:00:44: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:00:44: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Tue, 02 Aug 2022 16:00:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:00:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.10_summits.bed INFO @ Tue, 02 Aug 2022 16:00:46: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:01:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:01:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:01:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:01:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518330/SRX9518330.20_summits.bed INFO @ Tue, 02 Aug 2022 16:01:12: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 23 millis CompletedMACS2peakCalling