[2024-01-24 13:42:57,343] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,345] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,345] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a850a16-360e-43cd-82d7-fd77a32fbace/dqc_reference
[2024-01-24 13:42:58,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,648] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c4e87b3-6b32-4141-9e45-fc390488213a/GCF_008369105.1_ASM836910v1_genomic.fna.gz | prodigal -d GCF_008369105.1_ASM836910v1_genomic.fna/cds.fna -a GCF_008369105.1_ASM836910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:12,763] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:12,764] [INFO] Task started: HMMsearch
[2024-01-24 13:43:12,764] [INFO] Running command: hmmsearch --tblout GCF_008369105.1_ASM836910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a850a16-360e-43cd-82d7-fd77a32fbace/dqc_reference/reference_markers.hmm GCF_008369105.1_ASM836910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:13,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:13,077] [INFO] Found 6/6 markers.
[2024-01-24 13:43:13,121] [INFO] Query marker FASTA was written to GCF_008369105.1_ASM836910v1_genomic.fna/markers.fasta
[2024-01-24 13:43:13,122] [INFO] Task started: Blastn
[2024-01-24 13:43:13,122] [INFO] Running command: blastn -query GCF_008369105.1_ASM836910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a850a16-360e-43cd-82d7-fd77a32fbace/dqc_reference/reference_markers.fasta -out GCF_008369105.1_ASM836910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:13,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:13,970] [INFO] Selected 35 target genomes.
[2024-01-24 13:43:13,970] [INFO] Target genome list was writen to GCF_008369105.1_ASM836910v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:13,985] [INFO] Task started: fastANI
[2024-01-24 13:43:13,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c4e87b3-6b32-4141-9e45-fc390488213a/GCF_008369105.1_ASM836910v1_genomic.fna.gz --refList GCF_008369105.1_ASM836910v1_genomic.fna/target_genomes.txt --output GCF_008369105.1_ASM836910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:39,047] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:39,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a850a16-360e-43cd-82d7-fd77a32fbace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:39,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a850a16-360e-43cd-82d7-fd77a32fbace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:39,077] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:43:39,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:43:39,077] [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
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.9974	591	1443	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.9572	586	1443	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	79.2488	510	1443	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.1091	482	1443	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.0908	484	1443	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	78.9832	490	1443	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.9246	516	1443	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.8861	467	1443	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.8664	461	1443	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.8381	518	1443	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.8218	530	1443	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.6799	531	1443	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.4884	484	1443	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.4489	354	1443	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.3506	448	1443	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	78.3343	347	1443	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	78.271	427	1443	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.2288	448	1443	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	78.1914	403	1443	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	78.1648	358	1443	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	78.1538	402	1443	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.1429	426	1443	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.1238	385	1443	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0203	397	1443	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9659	346	1443	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	77.9311	327	1443	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.9085	418	1443	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.786	340	1443	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.6772	326	1443	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.2327	259	1443	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.4272	57	1443	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.3954	73	1443	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.1752	67	1443	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.1548	70	1443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:39,079] [INFO] DFAST Taxonomy check result was written to GCF_008369105.1_ASM836910v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:39,079] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:39,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:39,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a850a16-360e-43cd-82d7-fd77a32fbace/dqc_reference/checkm_data
[2024-01-24 13:43:39,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:39,126] [INFO] Task started: CheckM
[2024-01-24 13:43:39,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008369105.1_ASM836910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008369105.1_ASM836910v1_genomic.fna/checkm_input GCF_008369105.1_ASM836910v1_genomic.fna/checkm_result
[2024-01-24 13:44:26,211] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:26,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:26,232] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:26,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:26,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008369105.1_ASM836910v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:26,233] [INFO] Task started: Blastn
[2024-01-24 13:44:26,234] [INFO] Running command: blastn -query GCF_008369105.1_ASM836910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a850a16-360e-43cd-82d7-fd77a32fbace/dqc_reference/reference_markers_gtdb.fasta -out GCF_008369105.1_ASM836910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:27,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:27,590] [INFO] Selected 16 target genomes.
[2024-01-24 13:44:27,591] [INFO] Target genome list was writen to GCF_008369105.1_ASM836910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:27,616] [INFO] Task started: fastANI
[2024-01-24 13:44:27,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c4e87b3-6b32-4141-9e45-fc390488213a/GCF_008369105.1_ASM836910v1_genomic.fna.gz --refList GCF_008369105.1_ASM836910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008369105.1_ASM836910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:43,675] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:43,695] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:43,695] [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_008369105.1	s__Aquicoccus porphyridii	100.0	1441	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_011389685.1	s__Aquicoccus sp011389685	88.7349	851	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314705.1	s__Aquicoccus sp001314705	87.8249	939	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	81.8031	804	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.2717	699	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002925845.1	s__Roseovarius nitratireducens	79.2222	513	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	79.2109	506	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003417655.1	s__Lentibacter sp003417655	78.8685	478	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.5668	503	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	78.02	468	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	77.8922	430	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_015223355.1	s__Salipiger pacificus_B	77.6623	408	1443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	75.3954	73	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_900187975.1	s__Pseudomonas delhiensis	75.2659	73	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	75.1058	78	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_001457615.1	s__Pseudomonas aeruginosa	75.0993	73	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:43,697] [INFO] GTDB search result was written to GCF_008369105.1_ASM836910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:43,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:43,703] [INFO] DFAST_QC result json was written to GCF_008369105.1_ASM836910v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:43,703] [INFO] DFAST_QC completed!
[2024-01-24 13:44:43,703] [INFO] Total running time: 0h1m46s