Job ID = 12266690 SRX = SRX8622125 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18980123 spots for SRR12096685/SRR12096685.sra Written 18980123 spots for SRR12096685/SRR12096685.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267235 ("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: 00:36:48 18980123 reads; of these: 18980123 (100.00%) were paired; of these: 12382310 (65.24%) aligned concordantly 0 times 5175485 (27.27%) aligned concordantly exactly 1 time 1422328 (7.49%) aligned concordantly >1 times ---- 12382310 pairs aligned concordantly 0 times; of these: 1185893 (9.58%) aligned discordantly 1 time ---- 11196417 pairs aligned 0 times concordantly or discordantly; of these: 22392834 mates make up the pairs; of these: 20534465 (91.70%) aligned 0 times 625974 (2.80%) aligned exactly 1 time 1232395 (5.50%) aligned >1 times 45.91% overall alignment rate Time searching: 00:36:48 Overall time: 00:36:48 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] 971003 / 7738879 = 0.1255 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 09:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.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 09:56:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:56:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:57:07: 1000000 INFO @ Sat, 03 Apr 2021 09:57:16: 2000000 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 09:57:26: 3000000 INFO @ Sat, 03 Apr 2021 09:57:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.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 09:57:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:57:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:57:35: 4000000 INFO @ Sat, 03 Apr 2021 09:57:39: 1000000 INFO @ Sat, 03 Apr 2021 09:57:45: 5000000 INFO @ Sat, 03 Apr 2021 09:57:50: 2000000 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 09:57:55: 6000000 INFO @ Sat, 03 Apr 2021 09:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.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 09:57:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:57:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:58:01: 3000000 INFO @ Sat, 03 Apr 2021 09:58:05: 7000000 INFO @ Sat, 03 Apr 2021 09:58:11: 1000000 INFO @ Sat, 03 Apr 2021 09:58:12: 4000000 INFO @ Sat, 03 Apr 2021 09:58:15: 8000000 INFO @ Sat, 03 Apr 2021 09:58:24: 5000000 INFO @ Sat, 03 Apr 2021 09:58:25: 2000000 INFO @ Sat, 03 Apr 2021 09:58:25: 9000000 INFO @ Sat, 03 Apr 2021 09:58:35: 10000000 INFO @ Sat, 03 Apr 2021 09:58:35: 6000000 INFO @ Sat, 03 Apr 2021 09:58:38: 3000000 INFO @ Sat, 03 Apr 2021 09:58:45: 11000000 INFO @ Sat, 03 Apr 2021 09:58:47: 7000000 INFO @ Sat, 03 Apr 2021 09:58:51: 4000000 INFO @ Sat, 03 Apr 2021 09:58:54: 12000000 INFO @ Sat, 03 Apr 2021 09:58:58: 8000000 INFO @ Sat, 03 Apr 2021 09:59:04: 13000000 INFO @ Sat, 03 Apr 2021 09:59:05: 5000000 INFO @ Sat, 03 Apr 2021 09:59:09: 9000000 INFO @ Sat, 03 Apr 2021 09:59:13: 14000000 INFO @ Sat, 03 Apr 2021 09:59:18: 6000000 INFO @ Sat, 03 Apr 2021 09:59:21: 10000000 INFO @ Sat, 03 Apr 2021 09:59:23: 15000000 INFO @ Sat, 03 Apr 2021 09:59:28: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:59:28: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:59:28: #1 total tags in treatment: 5715651 INFO @ Sat, 03 Apr 2021 09:59:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:59:28: #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 09:59:28: #1 tags after filtering in treatment: 4990022 INFO @ Sat, 03 Apr 2021 09:59:28: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 09:59:28: #1 finished! INFO @ Sat, 03 Apr 2021 09:59:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:59:29: #2 number of paired peaks: 1231 INFO @ Sat, 03 Apr 2021 09:59:29: start model_add_line... INFO @ Sat, 03 Apr 2021 09:59:29: start X-correlation... INFO @ Sat, 03 Apr 2021 09:59:29: end of X-cor INFO @ Sat, 03 Apr 2021 09:59:29: #2 finished! INFO @ Sat, 03 Apr 2021 09:59:29: #2 predicted fragment length is 228 bps INFO @ Sat, 03 Apr 2021 09:59:29: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 03 Apr 2021 09:59:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.05_model.r WARNING @ Sat, 03 Apr 2021 09:59:29: #2 Since the d (228) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:59:29: #2 You may need to consider one of the other alternative d(s): 228 WARNING @ Sat, 03 Apr 2021 09:59:29: #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 09:59:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:59:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:59:32: 11000000 INFO @ Sat, 03 Apr 2021 09:59:32: 7000000 INFO @ Sat, 03 Apr 2021 09:59:42: 12000000 INFO @ Sat, 03 Apr 2021 09:59:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:59:45: 8000000 INFO @ Sat, 03 Apr 2021 09:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.05_summits.bed INFO @ Sat, 03 Apr 2021 09:59:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4798 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:59:53: 13000000 INFO @ Sat, 03 Apr 2021 09:59:59: 9000000 INFO @ Sat, 03 Apr 2021 10:00:05: 14000000 INFO @ Sat, 03 Apr 2021 10:00:12: 10000000 INFO @ Sat, 03 Apr 2021 10:00:16: 15000000 INFO @ Sat, 03 Apr 2021 10:00:22: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:00:22: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:00:22: #1 total tags in treatment: 5715651 INFO @ Sat, 03 Apr 2021 10:00:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:00:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 10:00:22: #1 tags after filtering in treatment: 4990022 INFO @ Sat, 03 Apr 2021 10:00:22: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 10:00:22: #1 finished! INFO @ Sat, 03 Apr 2021 10:00:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:00:22: #2 number of paired peaks: 1231 INFO @ Sat, 03 Apr 2021 10:00:22: start model_add_line... INFO @ Sat, 03 Apr 2021 10:00:23: start X-correlation... INFO @ Sat, 03 Apr 2021 10:00:23: end of X-cor INFO @ Sat, 03 Apr 2021 10:00:23: #2 finished! INFO @ Sat, 03 Apr 2021 10:00:23: #2 predicted fragment length is 228 bps INFO @ Sat, 03 Apr 2021 10:00:23: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 03 Apr 2021 10:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.10_model.r WARNING @ Sat, 03 Apr 2021 10:00:23: #2 Since the d (228) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:00:23: #2 You may need to consider one of the other alternative d(s): 228 WARNING @ Sat, 03 Apr 2021 10:00:23: #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 10:00:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:00:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:00:25: 11000000 INFO @ Sat, 03 Apr 2021 10:00:37: 12000000 INFO @ Sat, 03 Apr 2021 10:00:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.10_peaks.xls INFO @ Sat, 03 Apr 2021 10:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.10_summits.bed INFO @ Sat, 03 Apr 2021 10:00:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2009 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:00:49: 13000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 10:01:02: 14000000 INFO @ Sat, 03 Apr 2021 10:01:14: 15000000 INFO @ Sat, 03 Apr 2021 10:01:21: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:01:21: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:01:21: #1 total tags in treatment: 5715651 INFO @ Sat, 03 Apr 2021 10:01:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:01:21: #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 10:01:21: #1 tags after filtering in treatment: 4990022 INFO @ Sat, 03 Apr 2021 10:01:21: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 10:01:21: #1 finished! INFO @ Sat, 03 Apr 2021 10:01:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:01:21: #2 number of paired peaks: 1231 INFO @ Sat, 03 Apr 2021 10:01:21: start model_add_line... INFO @ Sat, 03 Apr 2021 10:01:21: start X-correlation... INFO @ Sat, 03 Apr 2021 10:01:21: end of X-cor INFO @ Sat, 03 Apr 2021 10:01:21: #2 finished! INFO @ Sat, 03 Apr 2021 10:01:21: #2 predicted fragment length is 228 bps INFO @ Sat, 03 Apr 2021 10:01:21: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 03 Apr 2021 10:01:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.20_model.r WARNING @ Sat, 03 Apr 2021 10:01:21: #2 Since the d (228) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:01:21: #2 You may need to consider one of the other alternative d(s): 228 WARNING @ Sat, 03 Apr 2021 10:01:21: #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 10:01:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:01:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.20_peaks.xls INFO @ Sat, 03 Apr 2021 10:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622125/SRX8622125.20_summits.bed INFO @ Sat, 03 Apr 2021 10:01:45: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 28 millis CompletedMACS2peakCalling