Job ID = 5720925 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T18:15:07 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T18:15:07 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T18:57:10 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T19:00:59 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T19:09:51 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T19:13:14 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T19:50:06 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T19:57:43 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T20:02:41 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T20:06:06 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 58,996,345 reads read : 117,992,690 reads written : 117,992,690 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:33:31 58996345 reads; of these: 58996345 (100.00%) were paired; of these: 12333320 (20.91%) aligned concordantly 0 times 37894176 (64.23%) aligned concordantly exactly 1 time 8768849 (14.86%) aligned concordantly >1 times ---- 12333320 pairs aligned concordantly 0 times; of these: 2647982 (21.47%) aligned discordantly 1 time ---- 9685338 pairs aligned 0 times concordantly or discordantly; of these: 19370676 mates make up the pairs; of these: 16160260 (83.43%) aligned 0 times 1660168 (8.57%) aligned exactly 1 time 1550248 (8.00%) aligned >1 times 86.30% overall alignment rate Time searching: 02:33:31 Overall time: 02:33:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 76 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 39755877 / 49203525 = 0.8080 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 08:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 08:22:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 08:22:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 08:23:05: 1000000 INFO @ Thu, 16 Apr 2020 08:23:15: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 08:23:25: 3000000 INFO @ Thu, 16 Apr 2020 08:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 08:23:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 08:23:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 08:23:35: 4000000 INFO @ Thu, 16 Apr 2020 08:23:36: 1000000 INFO @ Thu, 16 Apr 2020 08:23:45: 5000000 INFO @ Thu, 16 Apr 2020 08:23:46: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 08:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 08:23:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 08:23:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 08:23:56: 6000000 INFO @ Thu, 16 Apr 2020 08:23:57: 3000000 INFO @ Thu, 16 Apr 2020 08:24:07: 1000000 INFO @ Thu, 16 Apr 2020 08:24:07: 7000000 INFO @ Thu, 16 Apr 2020 08:24:08: 4000000 INFO @ Thu, 16 Apr 2020 08:24:18: 2000000 INFO @ Thu, 16 Apr 2020 08:24:18: 8000000 INFO @ Thu, 16 Apr 2020 08:24:19: 5000000 INFO @ Thu, 16 Apr 2020 08:24:29: 3000000 INFO @ Thu, 16 Apr 2020 08:24:29: 9000000 INFO @ Thu, 16 Apr 2020 08:24:31: 6000000 INFO @ Thu, 16 Apr 2020 08:24:40: 10000000 INFO @ Thu, 16 Apr 2020 08:24:40: 4000000 INFO @ Thu, 16 Apr 2020 08:24:42: 7000000 INFO @ Thu, 16 Apr 2020 08:24:51: 11000000 INFO @ Thu, 16 Apr 2020 08:24:51: 5000000 INFO @ Thu, 16 Apr 2020 08:24:53: 8000000 INFO @ Thu, 16 Apr 2020 08:25:02: 12000000 INFO @ Thu, 16 Apr 2020 08:25:02: 6000000 INFO @ Thu, 16 Apr 2020 08:25:04: 9000000 INFO @ Thu, 16 Apr 2020 08:25:13: 13000000 INFO @ Thu, 16 Apr 2020 08:25:14: 7000000 INFO @ Thu, 16 Apr 2020 08:25:16: 10000000 INFO @ Thu, 16 Apr 2020 08:25:24: 14000000 INFO @ Thu, 16 Apr 2020 08:25:25: 8000000 INFO @ Thu, 16 Apr 2020 08:25:27: 11000000 INFO @ Thu, 16 Apr 2020 08:25:35: 15000000 INFO @ Thu, 16 Apr 2020 08:25:36: 9000000 INFO @ Thu, 16 Apr 2020 08:25:38: 12000000 INFO @ Thu, 16 Apr 2020 08:25:47: 16000000 INFO @ Thu, 16 Apr 2020 08:25:47: 10000000 INFO @ Thu, 16 Apr 2020 08:25:49: 13000000 INFO @ Thu, 16 Apr 2020 08:25:58: 17000000 INFO @ Thu, 16 Apr 2020 08:25:58: 11000000 INFO @ Thu, 16 Apr 2020 08:26:01: 14000000 INFO @ Thu, 16 Apr 2020 08:26:09: 18000000 INFO @ Thu, 16 Apr 2020 08:26:10: 12000000 INFO @ Thu, 16 Apr 2020 08:26:12: 15000000 INFO @ Thu, 16 Apr 2020 08:26:20: 19000000 INFO @ Thu, 16 Apr 2020 08:26:21: 13000000 INFO @ Thu, 16 Apr 2020 08:26:23: 16000000 INFO @ Thu, 16 Apr 2020 08:26:31: 20000000 INFO @ Thu, 16 Apr 2020 08:26:32: 14000000 INFO @ Thu, 16 Apr 2020 08:26:34: 17000000 INFO @ Thu, 16 Apr 2020 08:26:42: 21000000 INFO @ Thu, 16 Apr 2020 08:26:43: 15000000 INFO @ Thu, 16 Apr 2020 08:26:45: 18000000 INFO @ Thu, 16 Apr 2020 08:26:53: 22000000 INFO @ Thu, 16 Apr 2020 08:26:55: 16000000 INFO @ Thu, 16 Apr 2020 08:26:56: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 08:26:56: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 08:26:56: #1 total tags in treatment: 8623807 INFO @ Thu, 16 Apr 2020 08:26:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:26:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 08:26:56: #1 tags after filtering in treatment: 8128747 INFO @ Thu, 16 Apr 2020 08:26:56: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 08:26:56: #1 finished! INFO @ Thu, 16 Apr 2020 08:26:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:26:57: 19000000 INFO @ Thu, 16 Apr 2020 08:26:57: #2 number of paired peaks: 1532 INFO @ Thu, 16 Apr 2020 08:26:57: start model_add_line... INFO @ Thu, 16 Apr 2020 08:26:57: start X-correlation... INFO @ Thu, 16 Apr 2020 08:26:57: end of X-cor INFO @ Thu, 16 Apr 2020 08:26:57: #2 finished! INFO @ Thu, 16 Apr 2020 08:26:57: #2 predicted fragment length is 266 bps INFO @ Thu, 16 Apr 2020 08:26:57: #2 alternative fragment length(s) may be 266 bps INFO @ Thu, 16 Apr 2020 08:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.05_model.r WARNING @ Thu, 16 Apr 2020 08:26:57: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 08:26:57: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Thu, 16 Apr 2020 08:26:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 08:26:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:27:06: 17000000 INFO @ Thu, 16 Apr 2020 08:27:07: 20000000 INFO @ Thu, 16 Apr 2020 08:27:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:27:16: 18000000 INFO @ Thu, 16 Apr 2020 08:27:18: 21000000 INFO @ Thu, 16 Apr 2020 08:27:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.05_peaks.xls INFO @ Thu, 16 Apr 2020 08:27:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:27:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.05_summits.bed INFO @ Thu, 16 Apr 2020 08:27:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7989 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 08:27:27: 19000000 INFO @ Thu, 16 Apr 2020 08:27:29: 22000000 INFO @ Thu, 16 Apr 2020 08:27:32: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 08:27:32: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 08:27:32: #1 total tags in treatment: 8623807 INFO @ Thu, 16 Apr 2020 08:27:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:27:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 08:27:32: #1 tags after filtering in treatment: 8128747 INFO @ Thu, 16 Apr 2020 08:27:32: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 08:27:32: #1 finished! INFO @ Thu, 16 Apr 2020 08:27:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:27:33: #2 number of paired peaks: 1532 INFO @ Thu, 16 Apr 2020 08:27:33: start model_add_line... INFO @ Thu, 16 Apr 2020 08:27:33: start X-correlation... INFO @ Thu, 16 Apr 2020 08:27:33: end of X-cor INFO @ Thu, 16 Apr 2020 08:27:33: #2 finished! INFO @ Thu, 16 Apr 2020 08:27:33: #2 predicted fragment length is 266 bps INFO @ Thu, 16 Apr 2020 08:27:33: #2 alternative fragment length(s) may be 266 bps INFO @ Thu, 16 Apr 2020 08:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.10_model.r WARNING @ Thu, 16 Apr 2020 08:27:33: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 08:27:33: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Thu, 16 Apr 2020 08:27:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 08:27:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:27:38: 20000000 INFO @ Thu, 16 Apr 2020 08:27:48: 21000000 INFO @ Thu, 16 Apr 2020 08:27:52: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:27:57: 22000000 INFO @ Thu, 16 Apr 2020 08:28:00: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 08:28:00: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 08:28:00: #1 total tags in treatment: 8623807 INFO @ Thu, 16 Apr 2020 08:28:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:28:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 08:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.10_peaks.xls INFO @ Thu, 16 Apr 2020 08:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:28:01: #1 tags after filtering in treatment: 8128747 INFO @ Thu, 16 Apr 2020 08:28:01: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 08:28:01: #1 finished! INFO @ Thu, 16 Apr 2020 08:28:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.10_summits.bed INFO @ Thu, 16 Apr 2020 08:28:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4991 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 08:28:01: #2 number of paired peaks: 1532 INFO @ Thu, 16 Apr 2020 08:28:01: start model_add_line... INFO @ Thu, 16 Apr 2020 08:28:01: start X-correlation... INFO @ Thu, 16 Apr 2020 08:28:01: end of X-cor INFO @ Thu, 16 Apr 2020 08:28:01: #2 finished! INFO @ Thu, 16 Apr 2020 08:28:01: #2 predicted fragment length is 266 bps INFO @ Thu, 16 Apr 2020 08:28:01: #2 alternative fragment length(s) may be 266 bps INFO @ Thu, 16 Apr 2020 08:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.20_model.r WARNING @ Thu, 16 Apr 2020 08:28:01: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 08:28:01: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Thu, 16 Apr 2020 08:28:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 08:28:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:28:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.20_peaks.xls INFO @ Thu, 16 Apr 2020 08:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386726/SRX6386726.20_summits.bed INFO @ Thu, 16 Apr 2020 08:28:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2716 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。