Job ID = 14160414 SRX = SRX9567193 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12569340 spots for SRR13125168/SRR13125168.sra Written 12569340 spots for SRR13125168/SRR13125168.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160595 ("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: 00:24:21 12569340 reads; of these: 12569340 (100.00%) were paired; of these: 6162829 (49.03%) aligned concordantly 0 times 5659013 (45.02%) aligned concordantly exactly 1 time 747498 (5.95%) aligned concordantly >1 times ---- 6162829 pairs aligned concordantly 0 times; of these: 4697710 (76.23%) aligned discordantly 1 time ---- 1465119 pairs aligned 0 times concordantly or discordantly; of these: 2930238 mates make up the pairs; of these: 990123 (33.79%) aligned 0 times 882189 (30.11%) aligned exactly 1 time 1057926 (36.10%) aligned >1 times 96.06% overall alignment rate Time searching: 00:24:22 Overall time: 00:24:22 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 20 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] 8322853 / 11099115 = 0.7499 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 02:48:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.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 02:48:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:48:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:03: 1000000 INFO @ Thu, 09 Dec 2021 02:49:11: 2000000 INFO @ Thu, 09 Dec 2021 02:49:18: 3000000 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 02:49:26: 4000000 INFO @ Thu, 09 Dec 2021 02:49:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.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 02:49:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:49:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:34: 5000000 INFO @ Thu, 09 Dec 2021 02:49:35: 1000000 INFO @ Thu, 09 Dec 2021 02:49:43: 6000000 INFO @ Thu, 09 Dec 2021 02:49:43: 2000000 INFO @ Thu, 09 Dec 2021 02:49:52: 7000000 INFO @ Thu, 09 Dec 2021 02:49:52: 3000000 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 02:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.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 02:49:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:49:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:56: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:49:56: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:49:56: #1 total tags in treatment: 1617051 INFO @ Thu, 09 Dec 2021 02:49:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:49:56: #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 02:49:56: #1 tags after filtering in treatment: 1526611 INFO @ Thu, 09 Dec 2021 02:49:56: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:49:56: #1 finished! INFO @ Thu, 09 Dec 2021 02:49:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:49:56: #2 number of paired peaks: 2478 INFO @ Thu, 09 Dec 2021 02:49:56: start model_add_line... INFO @ Thu, 09 Dec 2021 02:49:57: start X-correlation... INFO @ Thu, 09 Dec 2021 02:49:57: end of X-cor INFO @ Thu, 09 Dec 2021 02:49:57: #2 finished! INFO @ Thu, 09 Dec 2021 02:49:57: #2 predicted fragment length is 282 bps INFO @ Thu, 09 Dec 2021 02:49:57: #2 alternative fragment length(s) may be 282 bps INFO @ Thu, 09 Dec 2021 02:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.05_model.r WARNING @ Thu, 09 Dec 2021 02:49:57: #2 Since the d (282) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:49:57: #2 You may need to consider one of the other alternative d(s): 282 WARNING @ Thu, 09 Dec 2021 02:49:57: #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 02:49:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:50:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:50:01: 4000000 INFO @ Thu, 09 Dec 2021 02:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:50:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.05_summits.bed INFO @ Thu, 09 Dec 2021 02:50:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1228 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:50:05: 1000000 INFO @ Thu, 09 Dec 2021 02:50:10: 5000000 INFO @ Thu, 09 Dec 2021 02:50:14: 2000000 INFO @ Thu, 09 Dec 2021 02:50:19: 6000000 INFO @ Thu, 09 Dec 2021 02:50:23: 3000000 INFO @ Thu, 09 Dec 2021 02:50:28: 7000000 INFO @ Thu, 09 Dec 2021 02:50:31: 4000000 INFO @ Thu, 09 Dec 2021 02:50:32: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:50:32: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:50:32: #1 total tags in treatment: 1617051 INFO @ Thu, 09 Dec 2021 02:50:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:50:32: #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 02:50:32: #1 tags after filtering in treatment: 1526611 INFO @ Thu, 09 Dec 2021 02:50:32: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:50:32: #1 finished! INFO @ Thu, 09 Dec 2021 02:50:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:50:32: #2 number of paired peaks: 2478 INFO @ Thu, 09 Dec 2021 02:50:32: start model_add_line... INFO @ Thu, 09 Dec 2021 02:50:32: start X-correlation... INFO @ Thu, 09 Dec 2021 02:50:32: end of X-cor INFO @ Thu, 09 Dec 2021 02:50:32: #2 finished! INFO @ Thu, 09 Dec 2021 02:50:32: #2 predicted fragment length is 282 bps INFO @ Thu, 09 Dec 2021 02:50:32: #2 alternative fragment length(s) may be 282 bps INFO @ Thu, 09 Dec 2021 02:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.10_model.r WARNING @ Thu, 09 Dec 2021 02:50:32: #2 Since the d (282) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:50:32: #2 You may need to consider one of the other alternative d(s): 282 WARNING @ Thu, 09 Dec 2021 02:50:32: #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 02:50:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:50:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:50:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.10_summits.bed INFO @ Thu, 09 Dec 2021 02:50:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:50:40: 5000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:50:48: 6000000 INFO @ Thu, 09 Dec 2021 02:50:56: 7000000 INFO @ Thu, 09 Dec 2021 02:51:00: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:51:00: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:51:00: #1 total tags in treatment: 1617051 INFO @ Thu, 09 Dec 2021 02:51:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:51:00: #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 02:51:00: #1 tags after filtering in treatment: 1526611 INFO @ Thu, 09 Dec 2021 02:51:00: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:51:00: #1 finished! INFO @ Thu, 09 Dec 2021 02:51:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:51:00: #2 number of paired peaks: 2478 INFO @ Thu, 09 Dec 2021 02:51:00: start model_add_line... INFO @ Thu, 09 Dec 2021 02:51:00: start X-correlation... INFO @ Thu, 09 Dec 2021 02:51:00: end of X-cor INFO @ Thu, 09 Dec 2021 02:51:00: #2 finished! INFO @ Thu, 09 Dec 2021 02:51:00: #2 predicted fragment length is 282 bps INFO @ Thu, 09 Dec 2021 02:51:00: #2 alternative fragment length(s) may be 282 bps INFO @ Thu, 09 Dec 2021 02:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.20_model.r WARNING @ Thu, 09 Dec 2021 02:51:00: #2 Since the d (282) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:51:00: #2 You may need to consider one of the other alternative d(s): 282 WARNING @ Thu, 09 Dec 2021 02:51:00: #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 02:51:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:51:04: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567193/SRX9567193.20_summits.bed INFO @ Thu, 09 Dec 2021 02:51:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 1 millis CompletedMACS2peakCalling