Job ID = 14160339 SRX = SRX9567168 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19064285 spots for SRR13125143/SRR13125143.sra Written 19064285 spots for SRR13125143/SRR13125143.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160554 ("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: 00:50:47 19064285 reads; of these: 19064285 (100.00%) were paired; of these: 7668931 (40.23%) aligned concordantly 0 times 7318018 (38.39%) aligned concordantly exactly 1 time 4077336 (21.39%) aligned concordantly >1 times ---- 7668931 pairs aligned concordantly 0 times; of these: 4757262 (62.03%) aligned discordantly 1 time ---- 2911669 pairs aligned 0 times concordantly or discordantly; of these: 5823338 mates make up the pairs; of these: 3441237 (59.09%) aligned 0 times 1116307 (19.17%) aligned exactly 1 time 1265794 (21.74%) aligned >1 times 90.97% overall alignment rate Time searching: 00:50:47 Overall time: 00:50:47 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 28 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] 13141094 / 16135803 = 0.8144 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 02:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.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 02:34:16: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:34:16: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:34:24: 1000000 INFO @ Thu, 09 Dec 2021 02:34:32: 2000000 INFO @ Thu, 09 Dec 2021 02:34:40: 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 02:34:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.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 02:34:46: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:34:46: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:34:49: 4000000 INFO @ Thu, 09 Dec 2021 02:34:57: 1000000 INFO @ Thu, 09 Dec 2021 02:34:59: 5000000 INFO @ Thu, 09 Dec 2021 02:35:07: 2000000 INFO @ Thu, 09 Dec 2021 02:35:10: 6000000 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 02:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.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 02:35:16: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:35:16: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:35:17: 3000000 INFO @ Thu, 09 Dec 2021 02:35:20: 7000000 INFO @ Thu, 09 Dec 2021 02:35:27: 1000000 INFO @ Thu, 09 Dec 2021 02:35:27: 4000000 INFO @ Thu, 09 Dec 2021 02:35:31: 8000000 INFO @ Thu, 09 Dec 2021 02:35:35: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:35:35: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:35:35: #1 total tags in treatment: 2177790 INFO @ Thu, 09 Dec 2021 02:35:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:35:35: #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 02:35:35: #1 tags after filtering in treatment: 1538065 INFO @ Thu, 09 Dec 2021 02:35:35: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 09 Dec 2021 02:35:35: #1 finished! INFO @ Thu, 09 Dec 2021 02:35:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:35:35: #2 number of paired peaks: 1010 INFO @ Thu, 09 Dec 2021 02:35:35: start model_add_line... INFO @ Thu, 09 Dec 2021 02:35:35: start X-correlation... INFO @ Thu, 09 Dec 2021 02:35:35: end of X-cor INFO @ Thu, 09 Dec 2021 02:35:35: #2 finished! INFO @ Thu, 09 Dec 2021 02:35:35: #2 predicted fragment length is 288 bps INFO @ Thu, 09 Dec 2021 02:35:35: #2 alternative fragment length(s) may be 288 bps INFO @ Thu, 09 Dec 2021 02:35:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.05_model.r WARNING @ Thu, 09 Dec 2021 02:35:35: #2 Since the d (288) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:35:35: #2 You may need to consider one of the other alternative d(s): 288 WARNING @ Thu, 09 Dec 2021 02:35:35: #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 02:35:35: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:35:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:35:37: 2000000 INFO @ Thu, 09 Dec 2021 02:35:38: 5000000 INFO @ Thu, 09 Dec 2021 02:35:40: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:35:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:35:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.05_summits.bed INFO @ Thu, 09 Dec 2021 02:35:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (720 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:35:48: 3000000 INFO @ Thu, 09 Dec 2021 02:35:48: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:35:58: 4000000 INFO @ Thu, 09 Dec 2021 02:35:58: 7000000 INFO @ Thu, 09 Dec 2021 02:36:09: 5000000 INFO @ Thu, 09 Dec 2021 02:36:09: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:36:13: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:36:13: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:36:13: #1 total tags in treatment: 2177790 INFO @ Thu, 09 Dec 2021 02:36:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:36:13: #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 02:36:13: #1 tags after filtering in treatment: 1538065 INFO @ Thu, 09 Dec 2021 02:36:13: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 09 Dec 2021 02:36:13: #1 finished! INFO @ Thu, 09 Dec 2021 02:36:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:36:14: #2 number of paired peaks: 1010 INFO @ Thu, 09 Dec 2021 02:36:14: start model_add_line... INFO @ Thu, 09 Dec 2021 02:36:14: start X-correlation... INFO @ Thu, 09 Dec 2021 02:36:14: end of X-cor INFO @ Thu, 09 Dec 2021 02:36:14: #2 finished! INFO @ Thu, 09 Dec 2021 02:36:14: #2 predicted fragment length is 288 bps INFO @ Thu, 09 Dec 2021 02:36:14: #2 alternative fragment length(s) may be 288 bps INFO @ Thu, 09 Dec 2021 02:36:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.10_model.r WARNING @ Thu, 09 Dec 2021 02:36:14: #2 Since the d (288) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:36:14: #2 You may need to consider one of the other alternative d(s): 288 WARNING @ Thu, 09 Dec 2021 02:36:14: #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 02:36:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:36:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:36:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:36:19: 6000000 INFO @ Thu, 09 Dec 2021 02:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.10_summits.bed INFO @ Thu, 09 Dec 2021 02:36:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (526 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:36:29: 7000000 INFO @ Thu, 09 Dec 2021 02:36:37: 8000000 INFO @ Thu, 09 Dec 2021 02:36:40: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:36:40: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:36:40: #1 total tags in treatment: 2177790 INFO @ Thu, 09 Dec 2021 02:36:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:36:40: #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 02:36:40: #1 tags after filtering in treatment: 1538065 INFO @ Thu, 09 Dec 2021 02:36:40: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 09 Dec 2021 02:36:40: #1 finished! INFO @ Thu, 09 Dec 2021 02:36:40: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:36:40: #2 number of paired peaks: 1010 INFO @ Thu, 09 Dec 2021 02:36:40: start model_add_line... INFO @ Thu, 09 Dec 2021 02:36:40: start X-correlation... INFO @ Thu, 09 Dec 2021 02:36:40: end of X-cor INFO @ Thu, 09 Dec 2021 02:36:40: #2 finished! INFO @ Thu, 09 Dec 2021 02:36:40: #2 predicted fragment length is 288 bps INFO @ Thu, 09 Dec 2021 02:36:40: #2 alternative fragment length(s) may be 288 bps INFO @ Thu, 09 Dec 2021 02:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.20_model.r WARNING @ Thu, 09 Dec 2021 02:36:40: #2 Since the d (288) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:36:40: #2 You may need to consider one of the other alternative d(s): 288 WARNING @ Thu, 09 Dec 2021 02:36:40: #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 02:36:40: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:36:45: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567168/SRX9567168.20_summits.bed INFO @ Thu, 09 Dec 2021 02:36:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 1 millis CompletedMACS2peakCalling