Job ID = 14170273 SRX = SRX8556395 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13939828 spots for SRR12024951/SRR12024951.sra Written 13939828 spots for SRR12024951/SRR12024951.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170885 ("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: 00:50:45 13939828 reads; of these: 13939828 (100.00%) were paired; of these: 7369669 (52.87%) aligned concordantly 0 times 4151529 (29.78%) aligned concordantly exactly 1 time 2418630 (17.35%) aligned concordantly >1 times ---- 7369669 pairs aligned concordantly 0 times; of these: 707776 (9.60%) aligned discordantly 1 time ---- 6661893 pairs aligned 0 times concordantly or discordantly; of these: 13323786 mates make up the pairs; of these: 10581758 (79.42%) aligned 0 times 984191 (7.39%) aligned exactly 1 time 1757837 (13.19%) aligned >1 times 62.04% overall alignment rate Time searching: 00:50:45 Overall time: 00:50:45 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 16 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] 1913612 / 7144214 = 0.2679 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 07:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.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 07:06:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:06:41: 1000000 INFO @ Sat, 11 Dec 2021 07:06:53: 2000000 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 07:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.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 07:06:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:07:06: 3000000 INFO @ Sat, 11 Dec 2021 07:07:11: 1000000 INFO @ Sat, 11 Dec 2021 07:07:20: 4000000 INFO @ Sat, 11 Dec 2021 07:07:23: 2000000 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 07:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.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 07:07:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:07:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:07:33: 5000000 INFO @ Sat, 11 Dec 2021 07:07:36: 3000000 INFO @ Sat, 11 Dec 2021 07:07:42: 1000000 INFO @ Sat, 11 Dec 2021 07:07:47: 6000000 INFO @ Sat, 11 Dec 2021 07:07:48: 4000000 INFO @ Sat, 11 Dec 2021 07:07:54: 2000000 INFO @ Sat, 11 Dec 2021 07:08:01: 5000000 INFO @ Sat, 11 Dec 2021 07:08:01: 7000000 INFO @ Sat, 11 Dec 2021 07:08:07: 3000000 INFO @ Sat, 11 Dec 2021 07:08:13: 6000000 INFO @ Sat, 11 Dec 2021 07:08:15: 8000000 INFO @ Sat, 11 Dec 2021 07:08:20: 4000000 INFO @ Sat, 11 Dec 2021 07:08:26: 7000000 INFO @ Sat, 11 Dec 2021 07:08:29: 9000000 INFO @ Sat, 11 Dec 2021 07:08:32: 5000000 INFO @ Sat, 11 Dec 2021 07:08:39: 8000000 INFO @ Sat, 11 Dec 2021 07:08:44: 10000000 INFO @ Sat, 11 Dec 2021 07:08:45: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:08:52: 9000000 INFO @ Sat, 11 Dec 2021 07:08:57: 7000000 INFO @ Sat, 11 Dec 2021 07:08:58: 11000000 INFO @ Sat, 11 Dec 2021 07:09:05: 10000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:09:10: 8000000 INFO @ Sat, 11 Dec 2021 07:09:13: 12000000 INFO @ Sat, 11 Dec 2021 07:09:17: 11000000 INFO @ Sat, 11 Dec 2021 07:09:23: 9000000 INFO @ Sat, 11 Dec 2021 07:09:27: 13000000 INFO @ Sat, 11 Dec 2021 07:09:31: 12000000 INFO @ Sat, 11 Dec 2021 07:09:33: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:09:33: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:09:33: #1 total tags in treatment: 4748514 INFO @ Sat, 11 Dec 2021 07:09:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:09:33: #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 07:09:33: #1 tags after filtering in treatment: 4100359 INFO @ Sat, 11 Dec 2021 07:09:33: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 07:09:33: #1 finished! INFO @ Sat, 11 Dec 2021 07:09:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:09:34: #2 number of paired peaks: 3772 INFO @ Sat, 11 Dec 2021 07:09:34: start model_add_line... INFO @ Sat, 11 Dec 2021 07:09:34: start X-correlation... INFO @ Sat, 11 Dec 2021 07:09:34: end of X-cor INFO @ Sat, 11 Dec 2021 07:09:34: #2 finished! INFO @ Sat, 11 Dec 2021 07:09:34: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Dec 2021 07:09:34: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Dec 2021 07:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.05_model.r WARNING @ Sat, 11 Dec 2021 07:09:34: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:09:34: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 11 Dec 2021 07:09:34: #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 07:09:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:09:36: 10000000 INFO @ Sat, 11 Dec 2021 07:09:42: 13000000 INFO @ Sat, 11 Dec 2021 07:09:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:47: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:09:47: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:09:47: #1 total tags in treatment: 4748514 INFO @ Sat, 11 Dec 2021 07:09:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:09:47: #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 07:09:47: #1 tags after filtering in treatment: 4100359 INFO @ Sat, 11 Dec 2021 07:09:47: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 07:09:47: #1 finished! INFO @ Sat, 11 Dec 2021 07:09:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.05_summits.bed INFO @ Sat, 11 Dec 2021 07:09:48: Done! INFO @ Sat, 11 Dec 2021 07:09:48: #2 number of paired peaks: 3772 INFO @ Sat, 11 Dec 2021 07:09:48: start model_add_line... INFO @ Sat, 11 Dec 2021 07:09:48: 11000000 INFO @ Sat, 11 Dec 2021 07:09:48: start X-correlation... INFO @ Sat, 11 Dec 2021 07:09:48: end of X-cor INFO @ Sat, 11 Dec 2021 07:09:48: #2 finished! INFO @ Sat, 11 Dec 2021 07:09:48: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Dec 2021 07:09:48: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Dec 2021 07:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.10_model.r WARNING @ Sat, 11 Dec 2021 07:09:48: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:09:48: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 11 Dec 2021 07:09:48: #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 07:09:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:09:48: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (17886 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:09:58: 12000000 INFO @ Sat, 11 Dec 2021 07:09:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:10:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:10:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:10:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.10_summits.bed INFO @ Sat, 11 Dec 2021 07:10:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9137 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:10:07: 13000000 INFO @ Sat, 11 Dec 2021 07:10:11: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:10:11: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:10:11: #1 total tags in treatment: 4748514 INFO @ Sat, 11 Dec 2021 07:10:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:10:11: #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 07:10:11: #1 tags after filtering in treatment: 4100359 INFO @ Sat, 11 Dec 2021 07:10:11: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 07:10:11: #1 finished! INFO @ Sat, 11 Dec 2021 07:10:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:10:11: #2 number of paired peaks: 3772 INFO @ Sat, 11 Dec 2021 07:10:11: start model_add_line... INFO @ Sat, 11 Dec 2021 07:10:11: start X-correlation... INFO @ Sat, 11 Dec 2021 07:10:11: end of X-cor INFO @ Sat, 11 Dec 2021 07:10:11: #2 finished! INFO @ Sat, 11 Dec 2021 07:10:11: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Dec 2021 07:10:11: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Dec 2021 07:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.20_model.r WARNING @ Sat, 11 Dec 2021 07:10:11: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:10:11: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 11 Dec 2021 07:10:11: #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 07:10:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:10:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:10:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:10:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:10:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556395/SRX8556395.20_summits.bed INFO @ Sat, 11 Dec 2021 07:10:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2612 records, 4 fields): 5 millis CompletedMACS2peakCalling