[2024-01-24 12:21:57,439] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,444] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa9dd023-73d2-41f7-96f7-2baf380d8ba8/dqc_reference
[2024-01-24 12:21:58,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,813] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,813] [INFO] Running command: gunzip -c /var/lib/cwl/stge68ba838-9534-4151-9e9a-d273166bcad9/GCF_000019965.1_ASM1996v1_genomic.fna.gz | prodigal -d GCF_000019965.1_ASM1996v1_genomic.fna/cds.fna -a GCF_000019965.1_ASM1996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:36,461] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:36,462] [INFO] Task started: HMMsearch
[2024-01-24 12:22:36,462] [INFO] Running command: hmmsearch --tblout GCF_000019965.1_ASM1996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa9dd023-73d2-41f7-96f7-2baf380d8ba8/dqc_reference/reference_markers.hmm GCF_000019965.1_ASM1996v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:36,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:36,728] [INFO] Found 6/6 markers.
[2024-01-24 12:22:36,776] [INFO] Query marker FASTA was written to GCF_000019965.1_ASM1996v1_genomic.fna/markers.fasta
[2024-01-24 12:22:36,776] [INFO] Task started: Blastn
[2024-01-24 12:22:36,776] [INFO] Running command: blastn -query GCF_000019965.1_ASM1996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa9dd023-73d2-41f7-96f7-2baf380d8ba8/dqc_reference/reference_markers.fasta -out GCF_000019965.1_ASM1996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:37,500] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:37,503] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:37,504] [INFO] Target genome list was writen to GCF_000019965.1_ASM1996v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:37,510] [INFO] Task started: fastANI
[2024-01-24 12:22:37,510] [INFO] Running command: fastANI --query /var/lib/cwl/stge68ba838-9534-4151-9e9a-d273166bcad9/GCF_000019965.1_ASM1996v1_genomic.fna.gz --refList GCF_000019965.1_ASM1996v1_genomic.fna/target_genomes.txt --output GCF_000019965.1_ASM1996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:48,551] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:48,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa9dd023-73d2-41f7-96f7-2baf380d8ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:48,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa9dd023-73d2-41f7-96f7-2baf380d8ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:48,561] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:48,562] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:48,562] [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
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	100.0	1983	1985	95	conclusive
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.3437	155	1985	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.0837	203	1985	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.8336	196	1985	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.759	260	1985	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.6442	159	1985	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	74.8865	96	1985	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.806	98	1985	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	74.8031	99	1985	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	74.7397	86	1985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:48,565] [INFO] DFAST Taxonomy check result was written to GCF_000019965.1_ASM1996v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:48,566] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:48,566] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:48,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa9dd023-73d2-41f7-96f7-2baf380d8ba8/dqc_reference/checkm_data
[2024-01-24 12:22:48,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:48,625] [INFO] Task started: CheckM
[2024-01-24 12:22:48,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000019965.1_ASM1996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000019965.1_ASM1996v1_genomic.fna/checkm_input GCF_000019965.1_ASM1996v1_genomic.fna/checkm_result
[2024-01-24 12:24:22,953] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:22,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:22,977] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:22,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:22,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000019965.1_ASM1996v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:22,977] [INFO] Task started: Blastn
[2024-01-24 12:24:22,977] [INFO] Running command: blastn -query GCF_000019965.1_ASM1996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa9dd023-73d2-41f7-96f7-2baf380d8ba8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000019965.1_ASM1996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:24,155] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:24,159] [INFO] Selected 26 target genomes.
[2024-01-24 12:24:24,159] [INFO] Target genome list was writen to GCF_000019965.1_ASM1996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:24,178] [INFO] Task started: fastANI
[2024-01-24 12:24:24,178] [INFO] Running command: fastANI --query /var/lib/cwl/stge68ba838-9534-4151-9e9a-d273166bcad9/GCF_000019965.1_ASM1996v1_genomic.fna.gz --refList GCF_000019965.1_ASM1996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000019965.1_ASM1996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:44,121] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:44,141] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:44,141] [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_000019965.1	s__Opitutus terrae	100.0	1983	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903825285.1	s__Opi-474 sp903825285	78.2272	418	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
GCA_903839035.1	s__Opi-474 sp903839035	78.2212	322	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.67	99.48	0.93	0.89	8	-
GCA_903872505.1	s__Opi-474 sp903872505	78.1939	374	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_903830425.1	s__Opi-474 sp903830425	78.1718	355	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_016715765.1	s__UBA2377 sp016715765	78.0279	339	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239845.1	s__Opitutus sp018239845	78.0055	395	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903855985.1	s__Opi-474 sp903855985	77.9819	326	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903877135.1	s__Opitutus sp903877135	77.9443	362	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	99.97	99.95	0.97	0.97	4	-
GCA_016235555.1	s__ER46 sp016235555	77.8555	506	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793535.1	s__ER46 sp016793535	77.8126	379	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239675.1	s__Opi-474 sp018239675	77.7439	385	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	77.7365	343	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695305.1	s__CAITWF01 sp009695305	77.6506	317	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896015.1	s__CAITWF01 sp903896015	77.6376	367	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.72	99.39	0.95	0.93	8	-
GCA_903840415.1	s__CAITWF01 sp903840415	77.6311	345	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.98	99.98	0.98	0.97	3	-
GCA_009695065.1	s__ER46 sp009695065	77.5572	198	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	96.54	96.54	0.63	0.63	2	-
GCA_016794665.1	s__ER46 sp016794665	77.5532	365	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209255.1	s__ER46 sp016209255	77.5363	309	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952145.1	s__UBA2377 sp903952145	77.3569	261	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	99.61	99.61	0.90	0.90	2	-
GCA_016199925.1	s__JACQFT01 sp016199925	76.9344	282	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__JACQFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919985.1	s__Tous-C4FEB sp903919985	76.8988	165	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929355.1	s__CAIYUN01 sp903929355	76.7857	225	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYUN01	95.0	99.96	99.94	0.97	0.97	4	-
GCA_903916755.1	s__Palsa-1447 sp903916755	76.778	218	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.68	99.68	0.97	0.97	2	-
GCA_005792355.1	s__ER46 sp005792355	76.7424	307	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.97	99.97	0.97	0.97	2	-
GCA_013822585.1	s__Didemnitutus sp013822585	76.7397	185	1985	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:44,143] [INFO] GTDB search result was written to GCF_000019965.1_ASM1996v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:44,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:44,148] [INFO] DFAST_QC result json was written to GCF_000019965.1_ASM1996v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:44,148] [INFO] DFAST_QC completed!
[2024-01-24 12:24:44,148] [INFO] Total running time: 0h2m47s