Job ID = 6367689 SRX = SRX3923762 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:50 prefetch.2.10.7: 1) Downloading 'SRR6983684'... 2020-06-15T23:32:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:42 prefetch.2.10.7: 1) 'SRR6983684' was downloaded successfully 2020-06-15T23:38:42 prefetch.2.10.7: 'SRR6983684' has 0 unresolved dependencies Read 71485065 spots for SRR6983684/SRR6983684.sra Written 71485065 spots for SRR6983684/SRR6983684.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:09 71485065 reads; of these: 71485065 (100.00%) were unpaired; of these: 10098543 (14.13%) aligned 0 times 52459655 (73.39%) aligned exactly 1 time 8926867 (12.49%) aligned >1 times 85.87% overall alignment rate Time searching: 00:15:09 Overall time: 00:15:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 28 files... [bam_rmdupse_core] 56640996 / 61386522 = 0.9227 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, 16 Jun 2020 09:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 09:05:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:33: 1000000 INFO @ Tue, 16 Jun 2020 09:05:38: 2000000 INFO @ Tue, 16 Jun 2020 09:05:44: 3000000 INFO @ Tue, 16 Jun 2020 09:05:49: 4000000 INFO @ Tue, 16 Jun 2020 09:05:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:05:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:05:53: #1 total tags in treatment: 4745526 INFO @ Tue, 16 Jun 2020 09:05:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:05:53: #1 tags after filtering in treatment: 4745526 INFO @ Tue, 16 Jun 2020 09:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:54: #2 number of paired peaks: 1416 INFO @ Tue, 16 Jun 2020 09:05:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:54: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:05:54: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 16 Jun 2020 09:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.05_model.r WARNING @ Tue, 16 Jun 2020 09:05:54: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:54: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 16 Jun 2020 09:05:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:05:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:54: #3 Pre-compute pvalue-qvalue table... 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, 16 Jun 2020 09:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 09:05:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:02: 1000000 INFO @ Tue, 16 Jun 2020 09:06:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:08: 2000000 INFO @ Tue, 16 Jun 2020 09:06:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.05_summits.bed INFO @ Tue, 16 Jun 2020 09:06:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3264 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:14: 3000000 INFO @ Tue, 16 Jun 2020 09:06:19: 4000000 INFO @ Tue, 16 Jun 2020 09:06:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:06:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:06:23: #1 total tags in treatment: 4745526 INFO @ Tue, 16 Jun 2020 09:06:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:06:23: #1 tags after filtering in treatment: 4745526 INFO @ Tue, 16 Jun 2020 09:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:24: #2 number of paired peaks: 1416 INFO @ Tue, 16 Jun 2020 09:06:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:24: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:06:24: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 16 Jun 2020 09:06:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.10_model.r WARNING @ Tue, 16 Jun 2020 09:06:24: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:06:24: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 16 Jun 2020 09:06:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:06:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:24: #3 Pre-compute pvalue-qvalue table... 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, 16 Jun 2020 09:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 09:06:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:34: 1000000 INFO @ Tue, 16 Jun 2020 09:06:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:41: 2000000 INFO @ Tue, 16 Jun 2020 09:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.10_summits.bed INFO @ Tue, 16 Jun 2020 09:06:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1170 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:48: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:06:55: 4000000 INFO @ Tue, 16 Jun 2020 09:07:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:07:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:07:00: #1 total tags in treatment: 4745526 INFO @ Tue, 16 Jun 2020 09:07:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:07:00: #1 tags after filtering in treatment: 4745526 INFO @ Tue, 16 Jun 2020 09:07:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:00: #2 number of paired peaks: 1416 INFO @ Tue, 16 Jun 2020 09:07:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:01: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:07:01: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 16 Jun 2020 09:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.20_model.r WARNING @ Tue, 16 Jun 2020 09:07:01: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:01: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 16 Jun 2020 09:07:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:07:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:07:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3923762/SRX3923762.20_summits.bed INFO @ Tue, 16 Jun 2020 09:07:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (489 records, 4 fields): 1 millis CompletedMACS2peakCalling