Job ID = 6626747 SRX = SRX7351013 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22526749 spots for SRR10673643/SRR10673643.sra Written 22526749 spots for SRR10673643/SRR10673643.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627028 ("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: 00:09:52 22526749 reads; of these: 22526749 (100.00%) were unpaired; of these: 628197 (2.79%) aligned 0 times 14852018 (65.93%) aligned exactly 1 time 7046534 (31.28%) aligned >1 times 97.21% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 3395980 / 21898552 = 0.1551 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 08:51:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.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 08:51:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:51:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:51:26: 1000000 INFO @ Tue, 14 Jul 2020 08:51:32: 2000000 INFO @ Tue, 14 Jul 2020 08:51:38: 3000000 INFO @ Tue, 14 Jul 2020 08:51:44: 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 08:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.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 08:51:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:51:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:51:50: 5000000 INFO @ Tue, 14 Jul 2020 08:51:58: 6000000 INFO @ Tue, 14 Jul 2020 08:51:58: 1000000 INFO @ Tue, 14 Jul 2020 08:52:05: 7000000 INFO @ Tue, 14 Jul 2020 08:52:06: 2000000 INFO @ Tue, 14 Jul 2020 08:52:13: 8000000 INFO @ Tue, 14 Jul 2020 08:52:14: 3000000 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 08:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.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 08:52:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:52:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:52:21: 9000000 INFO @ Tue, 14 Jul 2020 08:52:21: 4000000 INFO @ Tue, 14 Jul 2020 08:52:28: 1000000 INFO @ Tue, 14 Jul 2020 08:52:28: 10000000 INFO @ Tue, 14 Jul 2020 08:52:29: 5000000 INFO @ Tue, 14 Jul 2020 08:52:36: 11000000 INFO @ Tue, 14 Jul 2020 08:52:36: 2000000 INFO @ Tue, 14 Jul 2020 08:52:37: 6000000 INFO @ Tue, 14 Jul 2020 08:52:44: 12000000 INFO @ Tue, 14 Jul 2020 08:52:44: 3000000 INFO @ Tue, 14 Jul 2020 08:52:45: 7000000 INFO @ Tue, 14 Jul 2020 08:52:51: 13000000 INFO @ Tue, 14 Jul 2020 08:52:52: 4000000 INFO @ Tue, 14 Jul 2020 08:52:53: 8000000 INFO @ Tue, 14 Jul 2020 08:52:59: 14000000 INFO @ Tue, 14 Jul 2020 08:53:00: 5000000 INFO @ Tue, 14 Jul 2020 08:53:01: 9000000 INFO @ Tue, 14 Jul 2020 08:53:07: 15000000 INFO @ Tue, 14 Jul 2020 08:53:08: 6000000 INFO @ Tue, 14 Jul 2020 08:53:09: 10000000 INFO @ Tue, 14 Jul 2020 08:53:15: 16000000 INFO @ Tue, 14 Jul 2020 08:53:16: 7000000 INFO @ Tue, 14 Jul 2020 08:53:18: 11000000 INFO @ Tue, 14 Jul 2020 08:53:23: 17000000 INFO @ Tue, 14 Jul 2020 08:53:24: 8000000 INFO @ Tue, 14 Jul 2020 08:53:26: 12000000 INFO @ Tue, 14 Jul 2020 08:53:31: 18000000 INFO @ Tue, 14 Jul 2020 08:53:32: 9000000 INFO @ Tue, 14 Jul 2020 08:53:34: 13000000 INFO @ Tue, 14 Jul 2020 08:53:35: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:53:35: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:53:35: #1 total tags in treatment: 18502572 INFO @ Tue, 14 Jul 2020 08:53:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:53:35: #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 08:53:35: #1 tags after filtering in treatment: 18502572 INFO @ Tue, 14 Jul 2020 08:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:53:35: #1 finished! INFO @ Tue, 14 Jul 2020 08:53:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:53:36: #2 number of paired peaks: 707 WARNING @ Tue, 14 Jul 2020 08:53:36: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Tue, 14 Jul 2020 08:53:36: start model_add_line... INFO @ Tue, 14 Jul 2020 08:53:36: start X-correlation... INFO @ Tue, 14 Jul 2020 08:53:36: end of X-cor INFO @ Tue, 14 Jul 2020 08:53:36: #2 finished! INFO @ Tue, 14 Jul 2020 08:53:36: #2 predicted fragment length is 75 bps INFO @ Tue, 14 Jul 2020 08:53:36: #2 alternative fragment length(s) may be 2,75 bps INFO @ Tue, 14 Jul 2020 08:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.05_model.r WARNING @ Tue, 14 Jul 2020 08:53:36: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:53:36: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Tue, 14 Jul 2020 08:53:36: #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 08:53:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:53:41: 10000000 INFO @ Tue, 14 Jul 2020 08:53:42: 14000000 INFO @ Tue, 14 Jul 2020 08:53:49: 11000000 INFO @ Tue, 14 Jul 2020 08:53:50: 15000000 INFO @ Tue, 14 Jul 2020 08:53:57: 12000000 INFO @ Tue, 14 Jul 2020 08:53:58: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:54:05: 13000000 INFO @ Tue, 14 Jul 2020 08:54:06: 17000000 INFO @ Tue, 14 Jul 2020 08:54:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:54:13: 14000000 INFO @ Tue, 14 Jul 2020 08:54:14: 18000000 INFO @ Tue, 14 Jul 2020 08:54:18: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:54:18: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:54:18: #1 total tags in treatment: 18502572 INFO @ Tue, 14 Jul 2020 08:54:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:54:18: #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 08:54:18: #1 tags after filtering in treatment: 18502572 INFO @ Tue, 14 Jul 2020 08:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:54:18: #1 finished! INFO @ Tue, 14 Jul 2020 08:54:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:54:20: #2 number of paired peaks: 707 WARNING @ Tue, 14 Jul 2020 08:54:20: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Tue, 14 Jul 2020 08:54:20: start model_add_line... INFO @ Tue, 14 Jul 2020 08:54:20: start X-correlation... INFO @ Tue, 14 Jul 2020 08:54:20: end of X-cor INFO @ Tue, 14 Jul 2020 08:54:20: #2 finished! INFO @ Tue, 14 Jul 2020 08:54:20: #2 predicted fragment length is 75 bps INFO @ Tue, 14 Jul 2020 08:54:20: #2 alternative fragment length(s) may be 2,75 bps INFO @ Tue, 14 Jul 2020 08:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.10_model.r WARNING @ Tue, 14 Jul 2020 08:54:20: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:54:20: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Tue, 14 Jul 2020 08:54:20: #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 08:54:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:54:21: 15000000 INFO @ Tue, 14 Jul 2020 08:54:28: 16000000 INFO @ Tue, 14 Jul 2020 08:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:54:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:54:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.05_summits.bed INFO @ Tue, 14 Jul 2020 08:54:31: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2955 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:54:36: 17000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:54:43: 18000000 INFO @ Tue, 14 Jul 2020 08:54:47: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:54:47: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:54:47: #1 total tags in treatment: 18502572 INFO @ Tue, 14 Jul 2020 08:54:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:54:47: #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 08:54:47: #1 tags after filtering in treatment: 18502572 INFO @ Tue, 14 Jul 2020 08:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:54:47: #1 finished! INFO @ Tue, 14 Jul 2020 08:54:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:54:48: #2 number of paired peaks: 707 WARNING @ Tue, 14 Jul 2020 08:54:48: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Tue, 14 Jul 2020 08:54:48: start model_add_line... INFO @ Tue, 14 Jul 2020 08:54:49: start X-correlation... INFO @ Tue, 14 Jul 2020 08:54:49: end of X-cor INFO @ Tue, 14 Jul 2020 08:54:49: #2 finished! INFO @ Tue, 14 Jul 2020 08:54:49: #2 predicted fragment length is 75 bps INFO @ Tue, 14 Jul 2020 08:54:49: #2 alternative fragment length(s) may be 2,75 bps INFO @ Tue, 14 Jul 2020 08:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.20_model.r WARNING @ Tue, 14 Jul 2020 08:54:49: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:54:49: #2 You may need to consider one of the other alternative d(s): 2,75 WARNING @ Tue, 14 Jul 2020 08:54:49: #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 08:54:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:54:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:55:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:55:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.10_summits.bed INFO @ Tue, 14 Jul 2020 08:55:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1788 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:55:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351013/SRX7351013.20_summits.bed INFO @ Tue, 14 Jul 2020 08:55:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (969 records, 4 fields): 2 millis CompletedMACS2peakCalling