[2023-03-16 18:14:24,283] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:14:24,283] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:14:24,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg75f44e6a-2f8f-49de-8cc6-d573c5cedfad/dqc_reference
[2023-03-16 18:14:25,474] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:14:25,475] [INFO] Task started: Prodigal
[2023-03-16 18:14:25,475] [INFO] Running command: cat /var/lib/cwl/stg044143e3-f246-4749-8b36-7ac05fb91447/OceanDNA-b34121.fa | prodigal -d OceanDNA-b34121/cds.fna -a OceanDNA-b34121/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:14:53,881] [INFO] Task succeeded: Prodigal
[2023-03-16 18:14:53,882] [INFO] Task started: HMMsearch
[2023-03-16 18:14:53,882] [INFO] Running command: hmmsearch --tblout OceanDNA-b34121/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75f44e6a-2f8f-49de-8cc6-d573c5cedfad/dqc_reference/reference_markers.hmm OceanDNA-b34121/protein.faa > /dev/null
[2023-03-16 18:14:54,110] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:14:54,111] [INFO] Found 6/6 markers.
[2023-03-16 18:14:54,135] [INFO] Query marker FASTA was written to OceanDNA-b34121/markers.fasta
[2023-03-16 18:14:54,136] [INFO] Task started: Blastn
[2023-03-16 18:14:54,136] [INFO] Running command: blastn -query OceanDNA-b34121/markers.fasta -db /var/lib/cwl/stg75f44e6a-2f8f-49de-8cc6-d573c5cedfad/dqc_reference/reference_markers.fasta -out OceanDNA-b34121/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:14:54,972] [INFO] Task succeeded: Blastn
[2023-03-16 18:14:54,973] [INFO] Selected 27 target genomes.
[2023-03-16 18:14:54,973] [INFO] Target genome list was writen to OceanDNA-b34121/target_genomes.txt
[2023-03-16 18:14:54,992] [INFO] Task started: fastANI
[2023-03-16 18:14:54,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg044143e3-f246-4749-8b36-7ac05fb91447/OceanDNA-b34121.fa --refList OceanDNA-b34121/target_genomes.txt --output OceanDNA-b34121/fastani_result.tsv --threads 1
[2023-03-16 18:15:15,962] [INFO] Task succeeded: fastANI
[2023-03-16 18:15:15,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75f44e6a-2f8f-49de-8cc6-d573c5cedfad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:15:15,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75f44e6a-2f8f-49de-8cc6-d573c5cedfad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:15:16,028] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:15:16,028] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:15:16,028] [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
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	80.4306	534	1475	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_012910815.1	41977	41977	type	True	80.4072	693	1475	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_003226565.1	41977	41977	type	True	80.3971	685	1475	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	80.3854	571	1475	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	80.3712	572	1475	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	80.3391	597	1475	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	80.1608	491	1475	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	80.1146	528	1475	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	80.0985	531	1475	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	80.0296	533	1475	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	79.9912	532	1475	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	79.943	517	1475	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	79.6776	567	1475	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	79.6091	568	1475	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.437	524	1475	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	79.3786	528	1475	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	79.3032	498	1475	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	78.964	482	1475	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.7468	447	1475	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.6255	460	1475	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.5838	408	1475	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.2177	351	1475	95	below_threshold
Pseudomonas extremorientalis		GCA_900625005.1	169669	169669	type	True	75.9889	91	1475	95	below_threshold
Pseudomonas extremorientalis	strain=LMG 19695	GCA_001870465.1	169669	169669	type	True	75.9889	91	1475	95	below_threshold
Pseudomonas extremorientalis	strain=CCUG 51517	GCA_008801565.1	169669	169669	type	True	75.9889	91	1475	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	75.7482	54	1475	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	75.4284	66	1475	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:15:16,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34121/tc_result.tsv
[2023-03-16 18:15:16,028] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:15:16,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:15:16,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75f44e6a-2f8f-49de-8cc6-d573c5cedfad/dqc_reference/checkm_data
[2023-03-16 18:15:16,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:15:16,035] [INFO] Task started: CheckM
[2023-03-16 18:15:16,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34121/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34121/checkm_input OceanDNA-b34121/checkm_result
[2023-03-16 18:16:58,021] [INFO] Task succeeded: CheckM
[2023-03-16 18:16:58,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:16:58,024] [INFO] ===== Completeness check finished =====
[2023-03-16 18:16:58,024] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:16:58,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34121/markers.fasta)
[2023-03-16 18:16:58,026] [INFO] Task started: Blastn
[2023-03-16 18:16:58,026] [INFO] Running command: blastn -query OceanDNA-b34121/markers.fasta -db /var/lib/cwl/stg75f44e6a-2f8f-49de-8cc6-d573c5cedfad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34121/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:16:59,656] [INFO] Task succeeded: Blastn
[2023-03-16 18:16:59,657] [INFO] Selected 17 target genomes.
[2023-03-16 18:16:59,658] [INFO] Target genome list was writen to OceanDNA-b34121/target_genomes_gtdb.txt
[2023-03-16 18:16:59,705] [INFO] Task started: fastANI
[2023-03-16 18:16:59,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg044143e3-f246-4749-8b36-7ac05fb91447/OceanDNA-b34121.fa --refList OceanDNA-b34121/target_genomes_gtdb.txt --output OceanDNA-b34121/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:17:15,365] [INFO] Task succeeded: fastANI
[2023-03-16 18:17:15,375] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:17:15,375] [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
GCF_003111645.1	s__Azoarcus_C communis_A	98.0925	1312	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	97.65	97.63	0.87	0.87	3	conclusive
GCF_003111665.1	s__Azoarcus_C communis_B	93.989	1290	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	98.41	98.41	0.92	0.92	2	-
GCF_018122735.1	s__Azoarcus_C sp018122735	83.1339	930	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006496635.1	s__Azoarcus sp006496635	80.7674	679	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	80.6221	572	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226565.1	s__Azoarcus_C communis	80.414	683	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	99.33	98.67	0.90	0.80	3	-
GCA_002422685.1	s__Thauera sp002422685	80.4021	519	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	80.3997	536	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	80.3886	570	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCF_001591165.1	s__Thauera butanivorans	80.361	573	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	80.2591	549	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696715.1	s__Thauera phenolivorans	79.9863	533	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCF_004361735.1	s__Azoarcus indigens	79.6594	569	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018824085.1	s__Methyloversatilis sp018824085	77.6302	248	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	99.98	99.98	0.99	0.99	4	-
GCF_001870465.1	s__Pseudomonas_E extremorientalis	75.9942	91	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	98.13	0.91	0.89	29	-
GCF_004327985.1	s__Marinobacter_A halodurans	75.4284	66	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:17:15,376] [INFO] GTDB search result was written to OceanDNA-b34121/result_gtdb.tsv
[2023-03-16 18:17:15,376] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:17:15,378] [INFO] DFAST_QC result json was written to OceanDNA-b34121/dqc_result.json
[2023-03-16 18:17:15,378] [INFO] DFAST_QC completed!
[2023-03-16 18:17:15,378] [INFO] Total running time: 0h2m51s