Job ID = 14160418 SRX = SRX9567197 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12265487 spots for SRR13125172/SRR13125172.sra Written 12265487 spots for SRR13125172/SRR13125172.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160602 ("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: 00:23:56 12265487 reads; of these: 12265487 (100.00%) were paired; of these: 4940937 (40.28%) aligned concordantly 0 times 6346171 (51.74%) aligned concordantly exactly 1 time 978379 (7.98%) aligned concordantly >1 times ---- 4940937 pairs aligned concordantly 0 times; of these: 3635794 (73.59%) aligned discordantly 1 time ---- 1305143 pairs aligned 0 times concordantly or discordantly; of these: 2610286 mates make up the pairs; of these: 1024673 (39.26%) aligned 0 times 739319 (28.32%) aligned exactly 1 time 846294 (32.42%) aligned >1 times 95.82% overall alignment rate Time searching: 00:23:56 Overall time: 00:23:56 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] 8455821 / 10956127 = 0.7718 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 02:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.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 02:49:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:49:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:59: 1000000 INFO @ Thu, 09 Dec 2021 02:50:06: 2000000 INFO @ Thu, 09 Dec 2021 02:50:14: 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 02:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.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 02:50:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:50:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:50:22: 4000000 INFO @ Thu, 09 Dec 2021 02:50:33: 5000000 INFO @ Thu, 09 Dec 2021 02:50:34: 1000000 INFO @ Thu, 09 Dec 2021 02:50:43: 6000000 INFO @ Thu, 09 Dec 2021 02:50:46: 2000000 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 02:50:50: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:50:50: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:50:50: #1 total tags in treatment: 1684602 INFO @ Thu, 09 Dec 2021 02:50:50: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:50:50: #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 02:50:50: #1 tags after filtering in treatment: 1562483 INFO @ Thu, 09 Dec 2021 02:50:50: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 02:50:50: #1 finished! INFO @ Thu, 09 Dec 2021 02:50:50: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:50:50: #2 number of paired peaks: 1986 INFO @ Thu, 09 Dec 2021 02:50:50: start model_add_line... INFO @ Thu, 09 Dec 2021 02:50:50: start X-correlation... INFO @ Thu, 09 Dec 2021 02:50:50: end of X-cor INFO @ Thu, 09 Dec 2021 02:50:50: #2 finished! INFO @ Thu, 09 Dec 2021 02:50:50: #2 predicted fragment length is 264 bps INFO @ Thu, 09 Dec 2021 02:50:50: #2 alternative fragment length(s) may be 264 bps INFO @ Thu, 09 Dec 2021 02:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.05_model.r WARNING @ Thu, 09 Dec 2021 02:50:50: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:50:50: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Thu, 09 Dec 2021 02:50:50: #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 02:50:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:50:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.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 02:50:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:50:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:50:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.05_summits.bed INFO @ Thu, 09 Dec 2021 02:50:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:50:58: 3000000 INFO @ Thu, 09 Dec 2021 02:51:02: 1000000 INFO @ Thu, 09 Dec 2021 02:51:11: 4000000 INFO @ Thu, 09 Dec 2021 02:51:13: 2000000 INFO @ Thu, 09 Dec 2021 02:51:23: 3000000 INFO @ Thu, 09 Dec 2021 02:51:24: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:51:34: 4000000 INFO @ Thu, 09 Dec 2021 02:51:36: 6000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:51:43: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:51:43: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:51:43: #1 total tags in treatment: 1684602 INFO @ Thu, 09 Dec 2021 02:51:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:51:43: #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 02:51:43: #1 tags after filtering in treatment: 1562483 INFO @ Thu, 09 Dec 2021 02:51:43: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 02:51:43: #1 finished! INFO @ Thu, 09 Dec 2021 02:51:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:51:44: #2 number of paired peaks: 1986 INFO @ Thu, 09 Dec 2021 02:51:44: start model_add_line... INFO @ Thu, 09 Dec 2021 02:51:44: start X-correlation... INFO @ Thu, 09 Dec 2021 02:51:44: end of X-cor INFO @ Thu, 09 Dec 2021 02:51:44: #2 finished! INFO @ Thu, 09 Dec 2021 02:51:44: #2 predicted fragment length is 264 bps INFO @ Thu, 09 Dec 2021 02:51:44: #2 alternative fragment length(s) may be 264 bps INFO @ Thu, 09 Dec 2021 02:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.10_model.r WARNING @ Thu, 09 Dec 2021 02:51:44: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:51:44: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Thu, 09 Dec 2021 02:51:44: #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 02:51:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:51:45: 5000000 INFO @ Thu, 09 Dec 2021 02:51:48: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.10_summits.bed INFO @ Thu, 09 Dec 2021 02:51:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:51:53: 6000000 INFO @ Thu, 09 Dec 2021 02:51:58: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:51:58: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:51:58: #1 total tags in treatment: 1684602 INFO @ Thu, 09 Dec 2021 02:51:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:51:58: #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 02:51:58: #1 tags after filtering in treatment: 1562483 INFO @ Thu, 09 Dec 2021 02:51:58: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 02:51:58: #1 finished! INFO @ Thu, 09 Dec 2021 02:51:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:51:58: #2 number of paired peaks: 1986 INFO @ Thu, 09 Dec 2021 02:51:58: start model_add_line... INFO @ Thu, 09 Dec 2021 02:51:58: start X-correlation... INFO @ Thu, 09 Dec 2021 02:51:58: end of X-cor INFO @ Thu, 09 Dec 2021 02:51:58: #2 finished! INFO @ Thu, 09 Dec 2021 02:51:58: #2 predicted fragment length is 264 bps INFO @ Thu, 09 Dec 2021 02:51:58: #2 alternative fragment length(s) may be 264 bps INFO @ Thu, 09 Dec 2021 02:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.20_model.r WARNING @ Thu, 09 Dec 2021 02:51:58: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:51:58: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Thu, 09 Dec 2021 02:51:58: #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 02:51:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:51:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:52:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:52:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:52:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:52:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567197/SRX9567197.20_summits.bed INFO @ Thu, 09 Dec 2021 02:52:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 14 millis CompletedMACS2peakCalling