[2023-03-15 11:54:50,925] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:54:50,925] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:54:50,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c12aaed-619c-4c43-a721-278a798dd68b/dqc_reference
[2023-03-15 11:54:52,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:54:52,057] [INFO] Task started: Prodigal
[2023-03-15 11:54:52,057] [INFO] Running command: cat /var/lib/cwl/stg8e79640d-e344-474c-95ea-e31e9e1a1435/OceanDNA-b10080.fa | prodigal -d OceanDNA-b10080/cds.fna -a OceanDNA-b10080/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:55:17,326] [INFO] Task succeeded: Prodigal
[2023-03-15 11:55:17,326] [INFO] Task started: HMMsearch
[2023-03-15 11:55:17,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b10080/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c12aaed-619c-4c43-a721-278a798dd68b/dqc_reference/reference_markers.hmm OceanDNA-b10080/protein.faa > /dev/null
[2023-03-15 11:55:17,559] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:55:17,560] [INFO] Found 6/6 markers.
[2023-03-15 11:55:17,589] [INFO] Query marker FASTA was written to OceanDNA-b10080/markers.fasta
[2023-03-15 11:55:17,592] [INFO] Task started: Blastn
[2023-03-15 11:55:17,592] [INFO] Running command: blastn -query OceanDNA-b10080/markers.fasta -db /var/lib/cwl/stg8c12aaed-619c-4c43-a721-278a798dd68b/dqc_reference/reference_markers.fasta -out OceanDNA-b10080/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:55:18,153] [INFO] Task succeeded: Blastn
[2023-03-15 11:55:18,157] [INFO] Selected 32 target genomes.
[2023-03-15 11:55:18,157] [INFO] Target genome list was writen to OceanDNA-b10080/target_genomes.txt
[2023-03-15 11:55:18,177] [INFO] Task started: fastANI
[2023-03-15 11:55:18,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e79640d-e344-474c-95ea-e31e9e1a1435/OceanDNA-b10080.fa --refList OceanDNA-b10080/target_genomes.txt --output OceanDNA-b10080/fastani_result.tsv --threads 1
[2023-03-15 11:55:41,984] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:41,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c12aaed-619c-4c43-a721-278a798dd68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:55:41,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c12aaed-619c-4c43-a721-278a798dd68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:55:41,998] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:55:41,998] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:55:41,998] [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
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	77.2601	186	1097	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	77.1724	191	1097	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	77.0024	189	1097	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	76.9984	155	1097	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	76.9676	172	1097	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	76.949	163	1097	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	76.8624	171	1097	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.8159	186	1097	95	below_threshold
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	76.7005	172	1097	95	below_threshold
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	76.6953	194	1097	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	76.6503	146	1097	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	76.4631	98	1097	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	76.455	95	1097	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	76.4291	89	1097	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	76.4029	80	1097	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	76.3579	82	1097	95	below_threshold
Ulvibacterium marinum	strain=CCMM003	GCA_003626755.1	2419782	2419782	type	True	76.3202	103	1097	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	76.2956	98	1097	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.2065	80	1097	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	76.1626	81	1097	95	below_threshold
Maribacter antarcticus	strain=DSM 21422	GCA_000621125.1	505250	505250	type	True	76.0814	72	1097	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	75.941	56	1097	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	75.7351	53	1097	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	75.6599	51	1097	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	75.2136	53	1097	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:55:42,000] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10080/tc_result.tsv
[2023-03-15 11:55:42,001] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:55:42,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:55:42,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c12aaed-619c-4c43-a721-278a798dd68b/dqc_reference/checkm_data
[2023-03-15 11:55:42,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:55:42,010] [INFO] Task started: CheckM
[2023-03-15 11:55:42,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10080/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10080/checkm_input OceanDNA-b10080/checkm_result
[2023-03-15 11:56:45,817] [INFO] Task succeeded: CheckM
[2023-03-15 11:56:45,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:56:45,882] [INFO] ===== Completeness check finished =====
[2023-03-15 11:56:45,882] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:56:45,882] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10080/markers.fasta)
[2023-03-15 11:56:45,902] [INFO] Task started: Blastn
[2023-03-15 11:56:45,902] [INFO] Running command: blastn -query OceanDNA-b10080/markers.fasta -db /var/lib/cwl/stg8c12aaed-619c-4c43-a721-278a798dd68b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10080/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:56:46,747] [INFO] Task succeeded: Blastn
[2023-03-15 11:56:46,751] [INFO] Selected 35 target genomes.
[2023-03-15 11:56:46,751] [INFO] Target genome list was writen to OceanDNA-b10080/target_genomes_gtdb.txt
[2023-03-15 11:56:46,863] [INFO] Task started: fastANI
[2023-03-15 11:56:46,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e79640d-e344-474c-95ea-e31e9e1a1435/OceanDNA-b10080.fa --refList OceanDNA-b10080/target_genomes_gtdb.txt --output OceanDNA-b10080/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:57:14,277] [INFO] Task succeeded: fastANI
[2023-03-15 11:57:14,294] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:57:14,294] [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_002813285.1	s__Pseudozobellia sp002813285	77.3765	228	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	77.2601	186	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_900156625.1	s__Zobellia uliginosa	77.1724	191	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017810075.1	s__Pseudozobellia sp017810075	77.1586	244	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860745.1	s__Zobellia uliginosa_B	77.0258	152	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725985.1	s__Zobellia amurskyensis	77.0024	189	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_014855495.1	s__Euzebyella saccharophila	76.9984	155	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330165.1	s__Zobellia sp015330165	76.9676	172	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_015330125.1	s__Zobellia sp015330125	76.9635	162	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_009725995.1	s__Zobellia laminariae	76.8624	171	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018728565.1	s__Zobellia russellii	76.8159	186	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_014855515.1	s__Euzebyella marina	76.7062	193	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_008367235.1	s__Pareuzebyella sediminis	76.7005	172	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pareuzebyella	95.0	99.39	99.39	0.97	0.97	2	-
GCF_900103215.1	s__Kriegella aquimaris	76.6645	145	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kriegella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349235.1	s__Euzebyella sp014349235	76.5213	167	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013402795.1	s__Costertonia aggregata	76.4631	98	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	76.455	95	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	76.4291	89	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	76.3787	81	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004364165.1	s__Maribacter spongiicola	76.2065	80	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	76.1626	81	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCA_003232155.1	s__RZ26 sp003232155	76.1359	52	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050085.1	s__Pricia antarctica_A	76.1267	125	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621125.1	s__Maribacter antarcticus	76.1046	71	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001430825.1	s__Sediminicola sp001430825	75.9972	69	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	75.941	56	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746415.1	s__Saonia sp002746415	75.7914	68	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	75.7135	54	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	75.6599	51	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_003581615.1	s__Muricauda lutimaris	75.652	57	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	75.5821	59	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	75.2136	53	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:57:14,296] [INFO] GTDB search result was written to OceanDNA-b10080/result_gtdb.tsv
[2023-03-15 11:57:14,298] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:57:14,303] [INFO] DFAST_QC result json was written to OceanDNA-b10080/dqc_result.json
[2023-03-15 11:57:14,303] [INFO] DFAST_QC completed!
[2023-03-15 11:57:14,303] [INFO] Total running time: 0h2m23s