[2023-03-18 01:03:22,772] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:03:22,773] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:03:22,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c6150f4-eee5-4927-bd95-93b9197984c6/dqc_reference
[2023-03-18 01:03:23,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:03:23,903] [INFO] Task started: Prodigal
[2023-03-18 01:03:23,903] [INFO] Running command: cat /var/lib/cwl/stg1bd1f5ba-062d-4153-a2d4-c9d7f6f3dd6f/OceanDNA-b33272.fa | prodigal -d OceanDNA-b33272/cds.fna -a OceanDNA-b33272/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:03:45,378] [INFO] Task succeeded: Prodigal
[2023-03-18 01:03:45,378] [INFO] Task started: HMMsearch
[2023-03-18 01:03:45,378] [INFO] Running command: hmmsearch --tblout OceanDNA-b33272/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c6150f4-eee5-4927-bd95-93b9197984c6/dqc_reference/reference_markers.hmm OceanDNA-b33272/protein.faa > /dev/null
[2023-03-18 01:03:45,590] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:03:45,590] [INFO] Found 6/6 markers.
[2023-03-18 01:03:45,610] [INFO] Query marker FASTA was written to OceanDNA-b33272/markers.fasta
[2023-03-18 01:03:45,612] [INFO] Task started: Blastn
[2023-03-18 01:03:45,612] [INFO] Running command: blastn -query OceanDNA-b33272/markers.fasta -db /var/lib/cwl/stg6c6150f4-eee5-4927-bd95-93b9197984c6/dqc_reference/reference_markers.fasta -out OceanDNA-b33272/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:03:46,368] [INFO] Task succeeded: Blastn
[2023-03-18 01:03:46,369] [INFO] Selected 26 target genomes.
[2023-03-18 01:03:46,369] [INFO] Target genome list was writen to OceanDNA-b33272/target_genomes.txt
[2023-03-18 01:03:46,385] [INFO] Task started: fastANI
[2023-03-18 01:03:46,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd1f5ba-062d-4153-a2d4-c9d7f6f3dd6f/OceanDNA-b33272.fa --refList OceanDNA-b33272/target_genomes.txt --output OceanDNA-b33272/fastani_result.tsv --threads 1
[2023-03-18 01:04:09,427] [INFO] Task succeeded: fastANI
[2023-03-18 01:04:09,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c6150f4-eee5-4927-bd95-93b9197984c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:04:09,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c6150f4-eee5-4927-bd95-93b9197984c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:04:09,442] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:04:09,442] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:04:09,442] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	78.696	364	1071	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.6637	365	1071	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	78.6556	363	1071	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	78.6344	365	1071	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	78.615	370	1071	95	below_threshold
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	78.5222	332	1071	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	78.4907	337	1071	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	78.4716	341	1071	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	78.4639	338	1071	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.4347	317	1071	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	78.4138	335	1071	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	78.4021	336	1071	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	78.3955	352	1071	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	78.3634	346	1071	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	78.3157	351	1071	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	78.3094	336	1071	95	below_threshold
Achromobacter mucicolens	strain=LMG 26685	GCA_902859725.1	1389922	1389922	type	True	78.2764	344	1071	95	below_threshold
Achromobacter aestuarii	strain=KS-M25	GCA_009866805.1	2511204	2511204	type	True	78.2607	319	1071	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	78.2446	337	1071	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	78.2246	338	1071	95	below_threshold
Achromobacter animicus	strain=LMG 26690	GCA_902859585.1	1389935	1389935	type	True	78.2054	346	1071	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.9462	185	1071	95	below_threshold
Bordetella flabilis	strain=AU10664	GCA_001676725.1	463014	463014	type	True	77.7582	271	1071	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.751	197	1071	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	76.3543	120	1071	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:04:09,442] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33272/tc_result.tsv
[2023-03-18 01:04:09,442] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:04:09,442] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:04:09,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c6150f4-eee5-4927-bd95-93b9197984c6/dqc_reference/checkm_data
[2023-03-18 01:04:09,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:04:09,447] [INFO] Task started: CheckM
[2023-03-18 01:04:09,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33272/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33272/checkm_input OceanDNA-b33272/checkm_result
[2023-03-18 01:05:03,889] [INFO] Task succeeded: CheckM
[2023-03-18 01:05:03,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:05:03,914] [INFO] ===== Completeness check finished =====
[2023-03-18 01:05:03,914] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:05:03,914] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33272/markers.fasta)
[2023-03-18 01:05:03,915] [INFO] Task started: Blastn
[2023-03-18 01:05:03,916] [INFO] Running command: blastn -query OceanDNA-b33272/markers.fasta -db /var/lib/cwl/stg6c6150f4-eee5-4927-bd95-93b9197984c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33272/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:05:05,306] [INFO] Task succeeded: Blastn
[2023-03-18 01:05:05,307] [INFO] Selected 26 target genomes.
[2023-03-18 01:05:05,307] [INFO] Target genome list was writen to OceanDNA-b33272/target_genomes_gtdb.txt
[2023-03-18 01:05:05,324] [INFO] Task started: fastANI
[2023-03-18 01:05:05,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd1f5ba-062d-4153-a2d4-c9d7f6f3dd6f/OceanDNA-b33272.fa --refList OceanDNA-b33272/target_genomes_gtdb.txt --output OceanDNA-b33272/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:05:28,910] [INFO] Task succeeded: fastANI
[2023-03-18 01:05:28,924] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:05:28,925] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_016462365.1	s__Achromobacter_A sp016462365	90.7423	636	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902905.1	s__Achromobacter sp002902905	78.5418	370	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.15	96.15	0.87	0.87	2	-
GCF_002885955.2	s__Achromobacter pulmonis_A	78.5378	359	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_900078705.1	s__Bordetella_B ansorpii_A	78.5194	372	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261475.1	s__Bordetella sp002261475	78.5128	343	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
GCF_014490035.1	s__Achromobacter bronchisepticus_A	78.5049	349	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_002209535.1	s__Achromobacter marplatensis	78.479	338	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.15	97.44	0.96	0.90	4	-
GCF_002261335.1	s__Bordetella sp002261335	78.4138	371	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_002975275.1	s__Achromobacter sp002975275	78.4008	323	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014170305.1	s__Achromobacter sp014170305	78.3957	350	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	78.3779	334	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_009763255.1	s__Bordetella_A sp009763255	78.3761	220	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	97.90	97.90	0.93	0.93	2	-
GCF_007679965.1	s__Bordetella_B sp007679965	78.3641	368	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	78.3521	347	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_017745595.1	s__Bordetella_A petrii_C	78.3438	329	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209485.1	s__Bordetella_C sp002209485	78.3034	317	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900496975.1	s__Achromobacter veterisilvae	78.2977	337	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001433395.1	s__Bordetella_C sp001433395	78.2916	325	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859725.1	s__Achromobacter mucicolens	78.2774	345	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.28	95.42	0.92	0.89	13	-
GCF_014170335.1	s__Achromobacter sp014170335	78.2746	346	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866805.1	s__Achromobacter_A aestuarii	78.2607	319	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012928505.1	s__Achromobacter sp012928505	78.2373	325	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428845.1	s__Achromobacter sp001428845	78.2232	344	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812705.1	s__Achromobacter spanius	78.2215	339	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.99	99.98	0.99	0.98	4	-
GCF_902859585.1	s__Achromobacter animicus	78.2041	345	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.58	96.10	0.93	0.89	8	-
GCF_002966795.1	s__Achromobacter spanius_D	78.1735	351	1071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	95.32	95.32	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:05:28,932] [INFO] GTDB search result was written to OceanDNA-b33272/result_gtdb.tsv
[2023-03-18 01:05:28,932] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:05:28,935] [INFO] DFAST_QC result json was written to OceanDNA-b33272/dqc_result.json
[2023-03-18 01:05:28,935] [INFO] DFAST_QC completed!
[2023-03-18 01:05:28,935] [INFO] Total running time: 0h2m6s