Job ID = 14160383 SRX = SRX8832088 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:23 12306543 reads; of these: 12306543 (100.00%) were unpaired; of these: 835751 (6.79%) aligned 0 times 9998008 (81.24%) aligned exactly 1 time 1472784 (11.97%) aligned >1 times 93.21% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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 8 files... [bam_rmdupse_core] 5297268 / 11470792 = 0.4618 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 @ Thu, 09 Dec 2021 02:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.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 @ Thu, 09 Dec 2021 02:05:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:05:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:05:36: 1000000 INFO @ Thu, 09 Dec 2021 02:05:42: 2000000 INFO @ Thu, 09 Dec 2021 02:05:48: 3000000 INFO @ Thu, 09 Dec 2021 02:05:53: 4000000 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 @ Thu, 09 Dec 2021 02:05:59: 5000000 INFO @ Thu, 09 Dec 2021 02:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.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 @ Thu, 09 Dec 2021 02:05:59: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:05:59: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:06:05: 6000000 INFO @ Thu, 09 Dec 2021 02:06:06: 1000000 INFO @ Thu, 09 Dec 2021 02:06:06: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:06:06: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:06:06: #1 total tags in treatment: 6173524 INFO @ Thu, 09 Dec 2021 02:06:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:06:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:06:07: #1 tags after filtering in treatment: 6173524 INFO @ Thu, 09 Dec 2021 02:06:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:06:07: #1 finished! INFO @ Thu, 09 Dec 2021 02:06:07: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:06:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:06:07: #2 number of paired peaks: 3534 INFO @ Thu, 09 Dec 2021 02:06:07: start model_add_line... INFO @ Thu, 09 Dec 2021 02:06:07: start X-correlation... INFO @ Thu, 09 Dec 2021 02:06:07: end of X-cor INFO @ Thu, 09 Dec 2021 02:06:07: #2 finished! INFO @ Thu, 09 Dec 2021 02:06:07: #2 predicted fragment length is 149 bps INFO @ Thu, 09 Dec 2021 02:06:07: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 09 Dec 2021 02:06:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.05_model.r INFO @ Thu, 09 Dec 2021 02:06:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:06:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:06:12: 2000000 INFO @ Thu, 09 Dec 2021 02:06:17: 3000000 INFO @ Thu, 09 Dec 2021 02:06:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:06:23: 4000000 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 @ Thu, 09 Dec 2021 02:06:28: 5000000 INFO @ Thu, 09 Dec 2021 02:06:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:06:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:06:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.05_summits.bed INFO @ Thu, 09 Dec 2021 02:06:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6743 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.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 @ Thu, 09 Dec 2021 02:06:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:06:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:06:35: 6000000 INFO @ Thu, 09 Dec 2021 02:06:37: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:06:37: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:06:37: #1 total tags in treatment: 6173524 INFO @ Thu, 09 Dec 2021 02:06:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:06:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:06:37: #1 tags after filtering in treatment: 6173524 INFO @ Thu, 09 Dec 2021 02:06:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:06:37: #1 finished! INFO @ Thu, 09 Dec 2021 02:06:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:06:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:06:37: 1000000 INFO @ Thu, 09 Dec 2021 02:06:37: #2 number of paired peaks: 3534 INFO @ Thu, 09 Dec 2021 02:06:37: start model_add_line... INFO @ Thu, 09 Dec 2021 02:06:37: start X-correlation... INFO @ Thu, 09 Dec 2021 02:06:37: end of X-cor INFO @ Thu, 09 Dec 2021 02:06:37: #2 finished! INFO @ Thu, 09 Dec 2021 02:06:37: #2 predicted fragment length is 149 bps INFO @ Thu, 09 Dec 2021 02:06:37: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 09 Dec 2021 02:06:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.10_model.r INFO @ Thu, 09 Dec 2021 02:06:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:06:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:06:44: 2000000 INFO @ Thu, 09 Dec 2021 02:06:52: 3000000 INFO @ Thu, 09 Dec 2021 02:06:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:06:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:06:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:06:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.10_summits.bed INFO @ Thu, 09 Dec 2021 02:06:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5562 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:06:59: 4000000 INFO @ Thu, 09 Dec 2021 02:07:06: 5000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:07:13: 6000000 INFO @ Thu, 09 Dec 2021 02:07:14: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:07:14: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:07:14: #1 total tags in treatment: 6173524 INFO @ Thu, 09 Dec 2021 02:07:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:07:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:07:14: #1 tags after filtering in treatment: 6173524 INFO @ Thu, 09 Dec 2021 02:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:07:14: #1 finished! INFO @ Thu, 09 Dec 2021 02:07:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:07:15: #2 number of paired peaks: 3534 INFO @ Thu, 09 Dec 2021 02:07:15: start model_add_line... INFO @ Thu, 09 Dec 2021 02:07:15: start X-correlation... INFO @ Thu, 09 Dec 2021 02:07:15: end of X-cor INFO @ Thu, 09 Dec 2021 02:07:15: #2 finished! INFO @ Thu, 09 Dec 2021 02:07:15: #2 predicted fragment length is 149 bps INFO @ Thu, 09 Dec 2021 02:07:15: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 09 Dec 2021 02:07:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.20_model.r INFO @ Thu, 09 Dec 2021 02:07:15: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:07:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832088/SRX8832088.20_summits.bed INFO @ Thu, 09 Dec 2021 02:07:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4331 records, 4 fields): 6 millis CompletedMACS2peakCalling