Job ID = 14160304 SRX = SRX9567202 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14893600 spots for SRR13125177/SRR13125177.sra Written 14893600 spots for SRR13125177/SRR13125177.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160484 ("srTce11") 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: 00:33:47 14893600 reads; of these: 14893600 (100.00%) were paired; of these: 6030997 (40.49%) aligned concordantly 0 times 8028980 (53.91%) aligned concordantly exactly 1 time 833623 (5.60%) aligned concordantly >1 times ---- 6030997 pairs aligned concordantly 0 times; of these: 4279611 (70.96%) aligned discordantly 1 time ---- 1751386 pairs aligned 0 times concordantly or discordantly; of these: 3502772 mates make up the pairs; of these: 1809370 (51.66%) aligned 0 times 812380 (23.19%) aligned exactly 1 time 881022 (25.15%) aligned >1 times 93.93% overall alignment rate Time searching: 00:33:47 Overall time: 00:33:47 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 24 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 9911204 / 13137326 = 0.7544 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 02:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.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 02:06:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:06:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:06:39: 1000000 INFO @ Thu, 09 Dec 2021 02:06:49: 2000000 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 02:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.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 02:06:58: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:06:58: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:07:00: 3000000 INFO @ Thu, 09 Dec 2021 02:07:11: 4000000 INFO @ Thu, 09 Dec 2021 02:07:15: 1000000 INFO @ Thu, 09 Dec 2021 02:07:22: 5000000 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 02:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.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 02:07:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:07:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:07:32: 2000000 INFO @ Thu, 09 Dec 2021 02:07:34: 6000000 INFO @ Thu, 09 Dec 2021 02:07:42: 1000000 INFO @ Thu, 09 Dec 2021 02:07:48: 7000000 INFO @ Thu, 09 Dec 2021 02:07:50: 3000000 INFO @ Thu, 09 Dec 2021 02:07:56: 2000000 INFO @ Thu, 09 Dec 2021 02:08:01: 8000000 INFO @ Thu, 09 Dec 2021 02:08:03: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:08:03: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:08:03: #1 total tags in treatment: 2157325 INFO @ Thu, 09 Dec 2021 02:08:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:08:03: #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 02:08:03: #1 tags after filtering in treatment: 2029008 INFO @ Thu, 09 Dec 2021 02:08:03: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:08:03: #1 finished! INFO @ Thu, 09 Dec 2021 02:08:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:08:04: #2 number of paired peaks: 2340 INFO @ Thu, 09 Dec 2021 02:08:04: start model_add_line... INFO @ Thu, 09 Dec 2021 02:08:04: start X-correlation... INFO @ Thu, 09 Dec 2021 02:08:04: end of X-cor INFO @ Thu, 09 Dec 2021 02:08:04: #2 finished! INFO @ Thu, 09 Dec 2021 02:08:04: #2 predicted fragment length is 283 bps INFO @ Thu, 09 Dec 2021 02:08:04: #2 alternative fragment length(s) may be 283 bps INFO @ Thu, 09 Dec 2021 02:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.05_model.r WARNING @ Thu, 09 Dec 2021 02:08:04: #2 Since the d (283) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:08:04: #2 You may need to consider one of the other alternative d(s): 283 WARNING @ Thu, 09 Dec 2021 02:08:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:08:04: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:08:08: 3000000 INFO @ Thu, 09 Dec 2021 02:08:08: 4000000 INFO @ Thu, 09 Dec 2021 02:08:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.05_summits.bed INFO @ Thu, 09 Dec 2021 02:08:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1535 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:08:19: 4000000 INFO @ Thu, 09 Dec 2021 02:08:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:08:30: 5000000 INFO @ Thu, 09 Dec 2021 02:08:40: 6000000 INFO @ Thu, 09 Dec 2021 02:08:41: 6000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:08:51: 7000000 INFO @ Thu, 09 Dec 2021 02:08:58: 7000000 INFO @ Thu, 09 Dec 2021 02:09:02: 8000000 INFO @ Thu, 09 Dec 2021 02:09:04: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:09:04: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:09:04: #1 total tags in treatment: 2157325 INFO @ Thu, 09 Dec 2021 02:09:04: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:09:04: #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 02:09:04: #1 tags after filtering in treatment: 2029008 INFO @ Thu, 09 Dec 2021 02:09:04: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:09:04: #1 finished! INFO @ Thu, 09 Dec 2021 02:09:04: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:09:04: #2 number of paired peaks: 2340 INFO @ Thu, 09 Dec 2021 02:09:04: start model_add_line... INFO @ Thu, 09 Dec 2021 02:09:04: start X-correlation... INFO @ Thu, 09 Dec 2021 02:09:04: end of X-cor INFO @ Thu, 09 Dec 2021 02:09:04: #2 finished! INFO @ Thu, 09 Dec 2021 02:09:04: #2 predicted fragment length is 283 bps INFO @ Thu, 09 Dec 2021 02:09:04: #2 alternative fragment length(s) may be 283 bps INFO @ Thu, 09 Dec 2021 02:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.20_model.r WARNING @ Thu, 09 Dec 2021 02:09:04: #2 Since the d (283) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:09:04: #2 You may need to consider one of the other alternative d(s): 283 WARNING @ Thu, 09 Dec 2021 02:09:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:09:04: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:09:11: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:09:14: 8000000 INFO @ Thu, 09 Dec 2021 02:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:09:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:09:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.20_summits.bed INFO @ Thu, 09 Dec 2021 02:09:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:09:16: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:09:16: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:09:16: #1 total tags in treatment: 2157325 INFO @ Thu, 09 Dec 2021 02:09:16: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:09:16: #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 02:09:16: #1 tags after filtering in treatment: 2029008 INFO @ Thu, 09 Dec 2021 02:09:16: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:09:16: #1 finished! INFO @ Thu, 09 Dec 2021 02:09:16: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:09:16: #2 number of paired peaks: 2340 INFO @ Thu, 09 Dec 2021 02:09:16: start model_add_line... INFO @ Thu, 09 Dec 2021 02:09:16: start X-correlation... INFO @ Thu, 09 Dec 2021 02:09:16: end of X-cor INFO @ Thu, 09 Dec 2021 02:09:16: #2 finished! INFO @ Thu, 09 Dec 2021 02:09:16: #2 predicted fragment length is 283 bps INFO @ Thu, 09 Dec 2021 02:09:16: #2 alternative fragment length(s) may be 283 bps INFO @ Thu, 09 Dec 2021 02:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.10_model.r WARNING @ Thu, 09 Dec 2021 02:09:16: #2 Since the d (283) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:09:16: #2 You may need to consider one of the other alternative d(s): 283 WARNING @ Thu, 09 Dec 2021 02:09:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:09:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:09:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567202/SRX9567202.10_summits.bed INFO @ Thu, 09 Dec 2021 02:09:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (720 records, 4 fields): 4 millis CompletedMACS2peakCalling