[2024-01-24 11:12:17,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:17,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:17,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg55a9b57e-adb8-4eab-86f3-f8706f2437e4/dqc_reference
[2024-01-24 11:12:18,981] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:18,981] [INFO] Task started: Prodigal
[2024-01-24 11:12:18,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg686900f7-73eb-48cc-afcb-bdb820979cb5/GCF_015182315.1_ASM1518231v1_genomic.fna.gz | prodigal -d GCF_015182315.1_ASM1518231v1_genomic.fna/cds.fna -a GCF_015182315.1_ASM1518231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:31,520] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:31,521] [INFO] Task started: HMMsearch
[2024-01-24 11:12:31,521] [INFO] Running command: hmmsearch --tblout GCF_015182315.1_ASM1518231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55a9b57e-adb8-4eab-86f3-f8706f2437e4/dqc_reference/reference_markers.hmm GCF_015182315.1_ASM1518231v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:31,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:31,794] [INFO] Found 6/6 markers.
[2024-01-24 11:12:31,835] [INFO] Query marker FASTA was written to GCF_015182315.1_ASM1518231v1_genomic.fna/markers.fasta
[2024-01-24 11:12:31,835] [INFO] Task started: Blastn
[2024-01-24 11:12:31,835] [INFO] Running command: blastn -query GCF_015182315.1_ASM1518231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55a9b57e-adb8-4eab-86f3-f8706f2437e4/dqc_reference/reference_markers.fasta -out GCF_015182315.1_ASM1518231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:32,648] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:32,653] [INFO] Selected 25 target genomes.
[2024-01-24 11:12:32,654] [INFO] Target genome list was writen to GCF_015182315.1_ASM1518231v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:34,688] [INFO] Task started: fastANI
[2024-01-24 11:12:34,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg686900f7-73eb-48cc-afcb-bdb820979cb5/GCF_015182315.1_ASM1518231v1_genomic.fna.gz --refList GCF_015182315.1_ASM1518231v1_genomic.fna/target_genomes.txt --output GCF_015182315.1_ASM1518231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:52,023] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:52,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55a9b57e-adb8-4eab-86f3-f8706f2437e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:52,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55a9b57e-adb8-4eab-86f3-f8706f2437e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:52,044] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:52,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:52,045] [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
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	100.0	1418	1420	95	conclusive
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	77.5693	200	1420	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	77.4215	141	1420	95	below_threshold
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	77.1828	107	1420	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	77.1554	110	1420	95	below_threshold
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	77.1173	127	1420	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	77.0216	73	1420	95	below_threshold
Aestuariicella hydrocarbonica	strain=JCM 30134	GCA_011602365.1	1470433	1470433	type	True	76.8794	80	1420	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	76.7349	65	1420	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.6125	99	1420	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	76.58	136	1420	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	76.5213	81	1420	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.4979	79	1420	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.2427	93	1420	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	76.1157	61	1420	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	75.8407	52	1420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:52,047] [INFO] DFAST Taxonomy check result was written to GCF_015182315.1_ASM1518231v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:52,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:52,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:52,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55a9b57e-adb8-4eab-86f3-f8706f2437e4/dqc_reference/checkm_data
[2024-01-24 11:12:52,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:52,092] [INFO] Task started: CheckM
[2024-01-24 11:12:52,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015182315.1_ASM1518231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015182315.1_ASM1518231v1_genomic.fna/checkm_input GCF_015182315.1_ASM1518231v1_genomic.fna/checkm_result
[2024-01-24 11:13:32,728] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:32,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:32,750] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:32,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:32,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015182315.1_ASM1518231v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:32,751] [INFO] Task started: Blastn
[2024-01-24 11:13:32,751] [INFO] Running command: blastn -query GCF_015182315.1_ASM1518231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55a9b57e-adb8-4eab-86f3-f8706f2437e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_015182315.1_ASM1518231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:34,050] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:34,055] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:34,055] [INFO] Target genome list was writen to GCF_015182315.1_ASM1518231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:34,614] [INFO] Task started: fastANI
[2024-01-24 11:13:34,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg686900f7-73eb-48cc-afcb-bdb820979cb5/GCF_015182315.1_ASM1518231v1_genomic.fna.gz --refList GCF_015182315.1_ASM1518231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015182315.1_ASM1518231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:45,760] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:45,776] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:45,777] [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_015182315.1	s__Cellvibrio polysaccharolyticus	100.0	1418	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002162135.1	s__Cellvibrio sp002162135	77.7795	253	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007605.1	s__Cellvibrio sp002007605	77.7756	217	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_004363885.1	s__Cellvibrio sp004363885	77.7417	207	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806955.1	s__Cellvibrio sp000263355	77.4803	210	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_014652535.1	s__Cellvibrio zantedeschiae	77.443	140	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953825.1	s__Cellvibrio sp000953825	77.2851	198	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858205.1	s__Cellvibrio sp903858205	77.1594	133	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762925.1	s__Marinimicrobium koreense	77.1361	126	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	96.56	95.81	0.88	0.87	5	-
GCA_004173475.1	s__Cellvibrio sp004173475	77.0502	100	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003524365.1	s__Cellvibrio sp003524365	76.8948	136	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483145.1	s__Cellvibrio sp002483145	76.88	189	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004172865.1	s__Cellvibrio sp004172865	76.7536	113	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	76.2373	92	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:45,778] [INFO] GTDB search result was written to GCF_015182315.1_ASM1518231v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:45,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:45,783] [INFO] DFAST_QC result json was written to GCF_015182315.1_ASM1518231v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:45,783] [INFO] DFAST_QC completed!
[2024-01-24 11:13:45,783] [INFO] Total running time: 0h1m28s