Job ID = 6626697 SRX = SRX7351011 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22252888 spots for SRR10673641/SRR10673641.sra Written 22252888 spots for SRR10673641/SRR10673641.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626977 ("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: 00:07:42 22252888 reads; of these: 22252888 (100.00%) were unpaired; of these: 638370 (2.87%) aligned 0 times 17775468 (79.88%) aligned exactly 1 time 3839050 (17.25%) aligned >1 times 97.13% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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 12 files... [bam_rmdupse_core] 5756641 / 21614518 = 0.2663 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:35:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.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, 14 Jul 2020 08:35:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:35:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:36:01: 1000000 INFO @ Tue, 14 Jul 2020 08:36:07: 2000000 INFO @ Tue, 14 Jul 2020 08:36:13: 3000000 INFO @ Tue, 14 Jul 2020 08:36:18: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:36:24: 5000000 INFO @ Tue, 14 Jul 2020 08:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.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, 14 Jul 2020 08:36:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:36:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:36:30: 6000000 INFO @ Tue, 14 Jul 2020 08:36:31: 1000000 INFO @ Tue, 14 Jul 2020 08:36:36: 7000000 INFO @ Tue, 14 Jul 2020 08:36:38: 2000000 INFO @ Tue, 14 Jul 2020 08:36:42: 8000000 INFO @ Tue, 14 Jul 2020 08:36:44: 3000000 INFO @ Tue, 14 Jul 2020 08:36:47: 9000000 INFO @ Tue, 14 Jul 2020 08:36:50: 4000000 INFO @ Tue, 14 Jul 2020 08:36:53: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.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, 14 Jul 2020 08:36:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:36:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:36:56: 5000000 INFO @ Tue, 14 Jul 2020 08:36:59: 11000000 INFO @ Tue, 14 Jul 2020 08:37:01: 1000000 INFO @ Tue, 14 Jul 2020 08:37:02: 6000000 INFO @ Tue, 14 Jul 2020 08:37:05: 12000000 INFO @ Tue, 14 Jul 2020 08:37:06: 2000000 INFO @ Tue, 14 Jul 2020 08:37:08: 7000000 INFO @ Tue, 14 Jul 2020 08:37:11: 13000000 INFO @ Tue, 14 Jul 2020 08:37:11: 3000000 INFO @ Tue, 14 Jul 2020 08:37:14: 8000000 INFO @ Tue, 14 Jul 2020 08:37:16: 4000000 INFO @ Tue, 14 Jul 2020 08:37:17: 14000000 INFO @ Tue, 14 Jul 2020 08:37:20: 9000000 INFO @ Tue, 14 Jul 2020 08:37:21: 5000000 INFO @ Tue, 14 Jul 2020 08:37:23: 15000000 INFO @ Tue, 14 Jul 2020 08:37:25: 10000000 INFO @ Tue, 14 Jul 2020 08:37:27: 6000000 INFO @ Tue, 14 Jul 2020 08:37:28: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:37:28: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:37:28: #1 total tags in treatment: 15857877 INFO @ Tue, 14 Jul 2020 08:37:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:37:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:37:28: #1 tags after filtering in treatment: 15857877 INFO @ Tue, 14 Jul 2020 08:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:37:28: #1 finished! INFO @ Tue, 14 Jul 2020 08:37:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:37:30: #2 number of paired peaks: 8365 INFO @ Tue, 14 Jul 2020 08:37:30: start model_add_line... INFO @ Tue, 14 Jul 2020 08:37:30: start X-correlation... INFO @ Tue, 14 Jul 2020 08:37:30: end of X-cor INFO @ Tue, 14 Jul 2020 08:37:30: #2 finished! INFO @ Tue, 14 Jul 2020 08:37:30: #2 predicted fragment length is 147 bps INFO @ Tue, 14 Jul 2020 08:37:30: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 14 Jul 2020 08:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.05_model.r WARNING @ Tue, 14 Jul 2020 08:37:30: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:37:30: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Tue, 14 Jul 2020 08:37:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:37:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:37:31: 11000000 INFO @ Tue, 14 Jul 2020 08:37:32: 7000000 INFO @ Tue, 14 Jul 2020 08:37:37: 8000000 INFO @ Tue, 14 Jul 2020 08:37:37: 12000000 INFO @ Tue, 14 Jul 2020 08:37:42: 9000000 INFO @ Tue, 14 Jul 2020 08:37:43: 13000000 INFO @ Tue, 14 Jul 2020 08:37:47: 10000000 INFO @ Tue, 14 Jul 2020 08:37:49: 14000000 INFO @ Tue, 14 Jul 2020 08:37:52: 11000000 INFO @ Tue, 14 Jul 2020 08:37:54: 15000000 INFO @ Tue, 14 Jul 2020 08:37:57: 12000000 INFO @ Tue, 14 Jul 2020 08:37:59: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:37:59: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:37:59: #1 total tags in treatment: 15857877 INFO @ Tue, 14 Jul 2020 08:37:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:37:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:37:59: #1 tags after filtering in treatment: 15857877 INFO @ Tue, 14 Jul 2020 08:37:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:37:59: #1 finished! INFO @ Tue, 14 Jul 2020 08:37:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:38:01: #2 number of paired peaks: 8365 INFO @ Tue, 14 Jul 2020 08:38:01: start model_add_line... INFO @ Tue, 14 Jul 2020 08:38:01: start X-correlation... INFO @ Tue, 14 Jul 2020 08:38:01: end of X-cor INFO @ Tue, 14 Jul 2020 08:38:01: #2 finished! INFO @ Tue, 14 Jul 2020 08:38:01: #2 predicted fragment length is 147 bps INFO @ Tue, 14 Jul 2020 08:38:01: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 14 Jul 2020 08:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.10_model.r WARNING @ Tue, 14 Jul 2020 08:38:01: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:38:01: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Tue, 14 Jul 2020 08:38:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:38:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:38:02: 13000000 INFO @ Tue, 14 Jul 2020 08:38:07: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:38:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:38:12: 15000000 INFO @ Tue, 14 Jul 2020 08:38:17: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:38:17: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:38:17: #1 total tags in treatment: 15857877 INFO @ Tue, 14 Jul 2020 08:38:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:38:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:38:17: #1 tags after filtering in treatment: 15857877 INFO @ Tue, 14 Jul 2020 08:38:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:38:17: #1 finished! INFO @ Tue, 14 Jul 2020 08:38:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:38:19: #2 number of paired peaks: 8365 INFO @ Tue, 14 Jul 2020 08:38:19: start model_add_line... INFO @ Tue, 14 Jul 2020 08:38:19: start X-correlation... INFO @ Tue, 14 Jul 2020 08:38:19: end of X-cor INFO @ Tue, 14 Jul 2020 08:38:19: #2 finished! INFO @ Tue, 14 Jul 2020 08:38:19: #2 predicted fragment length is 147 bps INFO @ Tue, 14 Jul 2020 08:38:19: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 14 Jul 2020 08:38:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.20_model.r WARNING @ Tue, 14 Jul 2020 08:38:19: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:38:19: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Tue, 14 Jul 2020 08:38:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:38:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:38:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.05_summits.bed INFO @ Tue, 14 Jul 2020 08:38:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14107 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:38:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:39:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:39:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:39:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.10_summits.bed INFO @ Tue, 14 Jul 2020 08:39:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11685 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:39:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351011/SRX7351011.20_summits.bed INFO @ Tue, 14 Jul 2020 08:39:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8048 records, 4 fields): 21 millis CompletedMACS2peakCalling