[2024-01-24 14:28:18,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,205] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg24c620d2-935d-42d3-bc69-1d1b33204aa5/dqc_reference
[2024-01-24 14:28:20,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,481] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg614afe9c-52ab-43ad-8c76-68dcd6e65fcf/GCF_000420045.1_ASM42004v1_genomic.fna.gz | prodigal -d GCF_000420045.1_ASM42004v1_genomic.fna/cds.fna -a GCF_000420045.1_ASM42004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:28,838] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:28,838] [INFO] Task started: HMMsearch
[2024-01-24 14:28:28,839] [INFO] Running command: hmmsearch --tblout GCF_000420045.1_ASM42004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24c620d2-935d-42d3-bc69-1d1b33204aa5/dqc_reference/reference_markers.hmm GCF_000420045.1_ASM42004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:29,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:29,090] [INFO] Found 6/6 markers.
[2024-01-24 14:28:29,139] [INFO] Query marker FASTA was written to GCF_000420045.1_ASM42004v1_genomic.fna/markers.fasta
[2024-01-24 14:28:29,139] [INFO] Task started: Blastn
[2024-01-24 14:28:29,139] [INFO] Running command: blastn -query GCF_000420045.1_ASM42004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24c620d2-935d-42d3-bc69-1d1b33204aa5/dqc_reference/reference_markers.fasta -out GCF_000420045.1_ASM42004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:30,257] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:30,261] [INFO] Selected 29 target genomes.
[2024-01-24 14:28:30,261] [INFO] Target genome list was writen to GCF_000420045.1_ASM42004v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:30,285] [INFO] Task started: fastANI
[2024-01-24 14:28:30,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg614afe9c-52ab-43ad-8c76-68dcd6e65fcf/GCF_000420045.1_ASM42004v1_genomic.fna.gz --refList GCF_000420045.1_ASM42004v1_genomic.fna/target_genomes.txt --output GCF_000420045.1_ASM42004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:50,044] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:50,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24c620d2-935d-42d3-bc69-1d1b33204aa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:50,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24c620d2-935d-42d3-bc69-1d1b33204aa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:50,073] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:28:50,073] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:28:50,074] [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
Fluviicoccus keumensis	strain=DSM 105135	GCA_004217445.1	1435465	1435465	type	True	78.6919	236	804	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.4409	239	804	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	78.3567	244	804	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	78.1761	247	804	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.1007	242	804	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	78.0029	245	804	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	77.9858	274	804	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	77.9758	278	804	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	77.9583	216	804	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.949	236	804	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.899	258	804	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	77.8732	273	804	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	77.8146	229	804	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	77.7004	202	804	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	77.6734	213	804	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	77.6545	202	804	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	77.652	222	804	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	77.6232	201	804	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	77.4905	179	804	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	77.4249	215	804	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	77.2192	186	804	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	77.2071	183	804	95	below_threshold
Paraperlucidibaca baekdonensis	strain=DSM 26022	GCA_003387535.1	748120	748120	type	True	77.1731	173	804	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.0092	135	804	95	below_threshold
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	76.9741	145	804	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.9154	134	804	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.908	129	804	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.8708	178	804	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.8393	130	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:50,076] [INFO] DFAST Taxonomy check result was written to GCF_000420045.1_ASM42004v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:50,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:50,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:50,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24c620d2-935d-42d3-bc69-1d1b33204aa5/dqc_reference/checkm_data
[2024-01-24 14:28:50,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:50,113] [INFO] Task started: CheckM
[2024-01-24 14:28:50,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420045.1_ASM42004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420045.1_ASM42004v1_genomic.fna/checkm_input GCF_000420045.1_ASM42004v1_genomic.fna/checkm_result
[2024-01-24 14:29:23,032] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:23,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:23,053] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:23,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:23,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420045.1_ASM42004v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:23,054] [INFO] Task started: Blastn
[2024-01-24 14:29:23,054] [INFO] Running command: blastn -query GCF_000420045.1_ASM42004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24c620d2-935d-42d3-bc69-1d1b33204aa5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420045.1_ASM42004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:25,066] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:25,069] [INFO] Selected 17 target genomes.
[2024-01-24 14:29:25,069] [INFO] Target genome list was writen to GCF_000420045.1_ASM42004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:25,082] [INFO] Task started: fastANI
[2024-01-24 14:29:25,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg614afe9c-52ab-43ad-8c76-68dcd6e65fcf/GCF_000420045.1_ASM42004v1_genomic.fna.gz --refList GCF_000420045.1_ASM42004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420045.1_ASM42004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:35,565] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:35,587] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:35,587] [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_000420045.1	s__Perlucidibaca piscinae	100.0	802	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002943415.1	s__Perlucidibaca sp002943415	84.483	387	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676655.1	s__Perlucidibaca aquatica	79.5955	269	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342025.1	s__Perlucidibaca sp002342025	79.2087	186	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217445.1	s__Fluviicoccus keumensis	78.7104	235	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Fluviicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262975.1	s__JADFDG01 sp018262975	78.438	234	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__JADFDG01;g__JADFDG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	78.3727	243	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	78.3276	255	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	78.2203	223	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	77.9904	214	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	77.8577	226	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_000265245.1	s__Halomonas smyrnensis	77.7149	201	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_015637705.1	s__Pseudomonas_E sp015637705	77.6224	186	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003543245.1	s__UBA2031 sp003543245	77.416	187	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__UBA2031	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	77.2685	182	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_003254665.1	s__Halomonas lactosivorans	77.2069	183	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865015.1	s__Sulfurisoma sediminicola	76.8886	130	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:35,589] [INFO] GTDB search result was written to GCF_000420045.1_ASM42004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:35,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:35,595] [INFO] DFAST_QC result json was written to GCF_000420045.1_ASM42004v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:35,595] [INFO] DFAST_QC completed!
[2024-01-24 14:29:35,595] [INFO] Total running time: 0h1m17s