Job ID = 14159578 SRX = SRX8845655 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6777971 spots for SRR12345962/SRR12345962.sra Written 6777971 spots for SRR12345962/SRR12345962.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159856 ("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: 00:08:08 6777971 reads; of these: 6777971 (100.00%) were paired; of these: 2653330 (39.15%) aligned concordantly 0 times 3440687 (50.76%) aligned concordantly exactly 1 time 683954 (10.09%) aligned concordantly >1 times ---- 2653330 pairs aligned concordantly 0 times; of these: 836402 (31.52%) aligned discordantly 1 time ---- 1816928 pairs aligned 0 times concordantly or discordantly; of these: 3633856 mates make up the pairs; of these: 3102324 (85.37%) aligned 0 times 221640 (6.10%) aligned exactly 1 time 309892 (8.53%) aligned >1 times 77.11% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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_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] 672681 / 4904815 = 0.1371 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 @ Wed, 08 Dec 2021 22:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.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 @ Wed, 08 Dec 2021 22:51:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:51:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:51:57: 1000000 INFO @ Wed, 08 Dec 2021 22:52:05: 2000000 INFO @ Wed, 08 Dec 2021 22:52:14: 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 @ Wed, 08 Dec 2021 22:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.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 @ Wed, 08 Dec 2021 22:52:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:52:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:52:23: 4000000 INFO @ Wed, 08 Dec 2021 22:52:29: 1000000 INFO @ Wed, 08 Dec 2021 22:52:32: 5000000 INFO @ Wed, 08 Dec 2021 22:52:37: 2000000 INFO @ Wed, 08 Dec 2021 22:52:41: 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 @ Wed, 08 Dec 2021 22:52:46: 3000000 INFO @ Wed, 08 Dec 2021 22:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.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 @ Wed, 08 Dec 2021 22:52:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:52:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:52:50: 7000000 INFO @ Wed, 08 Dec 2021 22:52:55: 4000000 INFO @ Wed, 08 Dec 2021 22:52:58: 1000000 INFO @ Wed, 08 Dec 2021 22:52:59: 8000000 INFO @ Wed, 08 Dec 2021 22:53:05: 5000000 INFO @ Wed, 08 Dec 2021 22:53:07: 2000000 INFO @ Wed, 08 Dec 2021 22:53:09: 9000000 INFO @ Wed, 08 Dec 2021 22:53:10: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:53:10: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:53:10: #1 total tags in treatment: 3581342 INFO @ Wed, 08 Dec 2021 22:53:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:53:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:53:10: #1 tags after filtering in treatment: 2752405 INFO @ Wed, 08 Dec 2021 22:53:10: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:53:10: #1 finished! INFO @ Wed, 08 Dec 2021 22:53:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:53:10: #2 number of paired peaks: 2770 INFO @ Wed, 08 Dec 2021 22:53:10: start model_add_line... INFO @ Wed, 08 Dec 2021 22:53:10: start X-correlation... INFO @ Wed, 08 Dec 2021 22:53:10: end of X-cor INFO @ Wed, 08 Dec 2021 22:53:10: #2 finished! INFO @ Wed, 08 Dec 2021 22:53:10: #2 predicted fragment length is 112 bps INFO @ Wed, 08 Dec 2021 22:53:10: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 08 Dec 2021 22:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.05_model.r WARNING @ Wed, 08 Dec 2021 22:53:10: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:53:10: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Wed, 08 Dec 2021 22:53:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:53:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:53:13: 6000000 INFO @ Wed, 08 Dec 2021 22:53:16: 3000000 INFO @ Wed, 08 Dec 2021 22:53:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:53:22: 7000000 INFO @ Wed, 08 Dec 2021 22:53:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:53:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:53:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.05_summits.bed INFO @ Wed, 08 Dec 2021 22:53:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6009 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:53:25: 4000000 INFO @ Wed, 08 Dec 2021 22:53:31: 8000000 INFO @ Wed, 08 Dec 2021 22:53:33: 5000000 INFO @ Wed, 08 Dec 2021 22:53:39: 9000000 INFO @ Wed, 08 Dec 2021 22:53:40: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:53:40: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:53:40: #1 total tags in treatment: 3581342 INFO @ Wed, 08 Dec 2021 22:53:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:53:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:53:40: #1 tags after filtering in treatment: 2752405 INFO @ Wed, 08 Dec 2021 22:53:40: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:53:40: #1 finished! INFO @ Wed, 08 Dec 2021 22:53:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:53:41: #2 number of paired peaks: 2770 INFO @ Wed, 08 Dec 2021 22:53:41: start model_add_line... INFO @ Wed, 08 Dec 2021 22:53:41: start X-correlation... INFO @ Wed, 08 Dec 2021 22:53:41: end of X-cor INFO @ Wed, 08 Dec 2021 22:53:41: #2 finished! INFO @ Wed, 08 Dec 2021 22:53:41: #2 predicted fragment length is 112 bps INFO @ Wed, 08 Dec 2021 22:53:41: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 08 Dec 2021 22:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.10_model.r WARNING @ Wed, 08 Dec 2021 22:53:41: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:53:41: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Wed, 08 Dec 2021 22:53:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:53:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:53:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:53:41: 6000000 INFO @ Wed, 08 Dec 2021 22:53:49: 7000000 INFO @ Wed, 08 Dec 2021 22:53:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:53:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:53:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:53:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.10_summits.bed INFO @ Wed, 08 Dec 2021 22:53:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3730 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:53:57: 8000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:54:06: 9000000 INFO @ Wed, 08 Dec 2021 22:54:06: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:54:06: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:54:06: #1 total tags in treatment: 3581342 INFO @ Wed, 08 Dec 2021 22:54:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:54:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:54:07: #1 tags after filtering in treatment: 2752405 INFO @ Wed, 08 Dec 2021 22:54:07: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:54:07: #1 finished! INFO @ Wed, 08 Dec 2021 22:54:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:54:07: #2 number of paired peaks: 2770 INFO @ Wed, 08 Dec 2021 22:54:07: start model_add_line... INFO @ Wed, 08 Dec 2021 22:54:07: start X-correlation... INFO @ Wed, 08 Dec 2021 22:54:07: end of X-cor INFO @ Wed, 08 Dec 2021 22:54:07: #2 finished! INFO @ Wed, 08 Dec 2021 22:54:07: #2 predicted fragment length is 112 bps INFO @ Wed, 08 Dec 2021 22:54:07: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 08 Dec 2021 22:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.20_model.r WARNING @ Wed, 08 Dec 2021 22:54:07: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:54:07: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Wed, 08 Dec 2021 22:54:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:54:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:54:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:54:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845655/SRX8845655.20_summits.bed INFO @ Wed, 08 Dec 2021 22:54:21: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1916 records, 4 fields): 4 millis CompletedMACS2peakCalling