[2024-01-24 12:44:52,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d929ccd-1ea8-4fa6-b777-fd4842159c7b/dqc_reference
[2024-01-24 12:44:53,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,831] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg0de8726f-3d72-4acb-b2b0-81ac1f99644d/GCF_008367235.1_ASM836723v1_genomic.fna.gz | prodigal -d GCF_008367235.1_ASM836723v1_genomic.fna/cds.fna -a GCF_008367235.1_ASM836723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:16,285] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:16,286] [INFO] Task started: HMMsearch
[2024-01-24 12:45:16,286] [INFO] Running command: hmmsearch --tblout GCF_008367235.1_ASM836723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d929ccd-1ea8-4fa6-b777-fd4842159c7b/dqc_reference/reference_markers.hmm GCF_008367235.1_ASM836723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:16,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:16,584] [INFO] Found 6/6 markers.
[2024-01-24 12:45:16,632] [INFO] Query marker FASTA was written to GCF_008367235.1_ASM836723v1_genomic.fna/markers.fasta
[2024-01-24 12:45:16,633] [INFO] Task started: Blastn
[2024-01-24 12:45:16,633] [INFO] Running command: blastn -query GCF_008367235.1_ASM836723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d929ccd-1ea8-4fa6-b777-fd4842159c7b/dqc_reference/reference_markers.fasta -out GCF_008367235.1_ASM836723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:17,254] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:17,259] [INFO] Selected 27 target genomes.
[2024-01-24 12:45:17,259] [INFO] Target genome list was writen to GCF_008367235.1_ASM836723v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:17,297] [INFO] Task started: fastANI
[2024-01-24 12:45:17,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg0de8726f-3d72-4acb-b2b0-81ac1f99644d/GCF_008367235.1_ASM836723v1_genomic.fna.gz --refList GCF_008367235.1_ASM836723v1_genomic.fna/target_genomes.txt --output GCF_008367235.1_ASM836723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:35,859] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:35,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d929ccd-1ea8-4fa6-b777-fd4842159c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:35,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d929ccd-1ea8-4fa6-b777-fd4842159c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:35,882] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:35,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:35,882] [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
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	100.0	1622	1623	95	conclusive
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	77.761	149	1623	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	77.6782	149	1623	95	below_threshold
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	77.4821	213	1623	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	77.3384	177	1623	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.0559	87	1623	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	76.9654	198	1623	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.9414	183	1623	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	76.9308	226	1623	95	below_threshold
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	76.8343	74	1623	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	76.8147	162	1623	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.7089	157	1623	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	76.6924	116	1623	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.594	88	1623	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	76.5481	110	1623	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.5214	81	1623	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.4833	81	1623	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.4389	116	1623	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.409	66	1623	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.2449	76	1623	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	75.9672	70	1623	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	75.8239	126	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:35,884] [INFO] DFAST Taxonomy check result was written to GCF_008367235.1_ASM836723v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:35,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:35,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:35,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d929ccd-1ea8-4fa6-b777-fd4842159c7b/dqc_reference/checkm_data
[2024-01-24 12:45:35,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:35,931] [INFO] Task started: CheckM
[2024-01-24 12:45:35,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008367235.1_ASM836723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008367235.1_ASM836723v1_genomic.fna/checkm_input GCF_008367235.1_ASM836723v1_genomic.fna/checkm_result
[2024-01-24 12:46:39,042] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:39,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:39,065] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:39,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:39,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008367235.1_ASM836723v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:39,066] [INFO] Task started: Blastn
[2024-01-24 12:46:39,066] [INFO] Running command: blastn -query GCF_008367235.1_ASM836723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d929ccd-1ea8-4fa6-b777-fd4842159c7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_008367235.1_ASM836723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:39,841] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:39,844] [INFO] Selected 24 target genomes.
[2024-01-24 12:46:39,844] [INFO] Target genome list was writen to GCF_008367235.1_ASM836723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:39,875] [INFO] Task started: fastANI
[2024-01-24 12:46:39,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg0de8726f-3d72-4acb-b2b0-81ac1f99644d/GCF_008367235.1_ASM836723v1_genomic.fna.gz --refList GCF_008367235.1_ASM836723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008367235.1_ASM836723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:56,377] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:56,408] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:56,409] [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_008367235.1	s__Pareuzebyella sediminis	100.0	1622	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pareuzebyella	95.0	99.39	99.39	0.97	0.97	2	conclusive
GCF_002269385.1	s__Maribacter cobaltidurans	77.7667	148	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014349235.1	s__Euzebyella sp014349235	77.567	171	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855515.1	s__Euzebyella marina	77.4688	214	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_014855495.1	s__Euzebyella saccharophila	77.3384	177	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	77.0559	87	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	76.9654	198	1623	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	76.9308	226	1623	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	76.9289	184	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_003001695.1	s__Muricauda pacifica	76.8343	74	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330125.1	s__Zobellia sp015330125	76.8147	162	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCA_002813285.1	s__Pseudozobellia sp002813285	76.7247	222	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101815.1	s__Pricia antarctica	76.71	158	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	76.5706	89	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	76.5471	80	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009371985.2	s__TP-CH-4 sp009371985	76.4389	116	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TP-CH-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	76.3262	87	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001430825.1	s__Sediminicola sp001430825	76.2712	100	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.2669	77	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	76.0798	87	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	76.0216	125	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	75.9694	73	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
GCF_900141935.1	s__Arenibacter nanhaiticus	75.8756	90	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	75.8147	127	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:56,410] [INFO] GTDB search result was written to GCF_008367235.1_ASM836723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:56,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:56,415] [INFO] DFAST_QC result json was written to GCF_008367235.1_ASM836723v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:56,415] [INFO] DFAST_QC completed!
[2024-01-24 12:46:56,415] [INFO] Total running time: 0h2m4s