[2024-01-24 13:32:30,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:30,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:30,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgd84e7aba-1768-43ee-b7c9-a4c20ee65fa8/dqc_reference
[2024-01-24 13:32:32,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:32,084] [INFO] Task started: Prodigal
[2024-01-24 13:32:32,084] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1053762-9646-433c-ae98-073667faa2f4/GCF_030450055.1_ASM3045005v1_genomic.fna.gz | prodigal -d GCF_030450055.1_ASM3045005v1_genomic.fna/cds.fna -a GCF_030450055.1_ASM3045005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:45,403] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:45,404] [INFO] Task started: HMMsearch
[2024-01-24 13:32:45,404] [INFO] Running command: hmmsearch --tblout GCF_030450055.1_ASM3045005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd84e7aba-1768-43ee-b7c9-a4c20ee65fa8/dqc_reference/reference_markers.hmm GCF_030450055.1_ASM3045005v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:45,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:45,736] [INFO] Found 6/6 markers.
[2024-01-24 13:32:45,780] [INFO] Query marker FASTA was written to GCF_030450055.1_ASM3045005v1_genomic.fna/markers.fasta
[2024-01-24 13:32:45,780] [INFO] Task started: Blastn
[2024-01-24 13:32:45,780] [INFO] Running command: blastn -query GCF_030450055.1_ASM3045005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd84e7aba-1768-43ee-b7c9-a4c20ee65fa8/dqc_reference/reference_markers.fasta -out GCF_030450055.1_ASM3045005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:46,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:46,972] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:46,972] [INFO] Target genome list was writen to GCF_030450055.1_ASM3045005v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:46,980] [INFO] Task started: fastANI
[2024-01-24 13:32:46,980] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1053762-9646-433c-ae98-073667faa2f4/GCF_030450055.1_ASM3045005v1_genomic.fna.gz --refList GCF_030450055.1_ASM3045005v1_genomic.fna/target_genomes.txt --output GCF_030450055.1_ASM3045005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:05,495] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:05,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd84e7aba-1768-43ee-b7c9-a4c20ee65fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:05,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd84e7aba-1768-43ee-b7c9-a4c20ee65fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:05,513] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:05,513] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:05,513] [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
Gallaecimonas xiamenensis	strain=3-C-1	GCA_000299915.1	1207039	1207039	type	True	83.239	860	1278	95	below_threshold
Gallaecimonas pentaromativorans	strain=DSM 21945	GCA_003751625.1	584787	584787	type	True	81.0775	754	1278	95	below_threshold
Gallaecimonas mangrovi	strain=HK-28	GCA_003367375.1	2291597	2291597	type	True	78.9182	354	1278	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	77.9825	287	1278	95	below_threshold
Aeromonas eucrenophila	strain=CECT 4224	GCA_000819865.1	649	649	type	True	77.9646	287	1278	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	77.9496	313	1278	95	below_threshold
Aeromonas simiae	strain=CIP 107798	GCA_000820125.1	218936	218936	type	True	77.8658	248	1278	95	below_threshold
Aeromonas bivalvium	strain=CECT 7113	GCA_000819765.1	440079	440079	type	True	77.8325	319	1278	95	below_threshold
Aeromonas encheleia	strain=CECT 4342	GCA_000819825.1	73010	73010	type	True	77.8058	315	1278	95	below_threshold
Ferrimonas balearica	strain=DSM 9799	GCA_000148645.1	44012	44012	type	True	77.7953	212	1278	95	below_threshold
Aeromonas diversa	strain=CECT 4254	GCA_000819805.1	502790	502790	type	True	77.7446	274	1278	95	below_threshold
Aeromonas diversa	strain=2478-85	GCA_000367845.1	502790	502790	type	True	77.7425	267	1278	95	below_threshold
Aeromonas schubertii	strain=CECT 4240	GCA_000820105.2	652	652	type	True	77.7203	281	1278	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	77.6733	304	1278	95	below_threshold
Aeromonas schubertii	strain=ATCC 43700	GCA_001481395.1	652	652	type	True	77.6644	277	1278	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	77.4929	287	1278	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.2387	264	1278	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.1845	187	1278	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	77.1332	136	1278	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	77.1111	236	1278	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.834	219	1278	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	76.7034	131	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:05,515] [INFO] DFAST Taxonomy check result was written to GCF_030450055.1_ASM3045005v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:05,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:05,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:05,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd84e7aba-1768-43ee-b7c9-a4c20ee65fa8/dqc_reference/checkm_data
[2024-01-24 13:33:05,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:05,561] [INFO] Task started: CheckM
[2024-01-24 13:33:05,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030450055.1_ASM3045005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030450055.1_ASM3045005v1_genomic.fna/checkm_input GCF_030450055.1_ASM3045005v1_genomic.fna/checkm_result
[2024-01-24 13:33:47,645] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:47,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:47,668] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:47,668] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:47,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030450055.1_ASM3045005v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:47,669] [INFO] Task started: Blastn
[2024-01-24 13:33:47,669] [INFO] Running command: blastn -query GCF_030450055.1_ASM3045005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd84e7aba-1768-43ee-b7c9-a4c20ee65fa8/dqc_reference/reference_markers_gtdb.fasta -out GCF_030450055.1_ASM3045005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:49,548] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:49,552] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:49,552] [INFO] Target genome list was writen to GCF_030450055.1_ASM3045005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:49,589] [INFO] Task started: fastANI
[2024-01-24 13:33:49,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1053762-9646-433c-ae98-073667faa2f4/GCF_030450055.1_ASM3045005v1_genomic.fna.gz --refList GCF_030450055.1_ASM3045005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030450055.1_ASM3045005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:03,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:03,492] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:34:03,493] [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_000299915.1	s__Gallaecimonas xiamenensis	83.2539	858	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751625.1	s__Gallaecimonas pentaromativorans	81.0694	755	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	98.58	98.58	0.94	0.94	2	-
GCF_003367375.1	s__Gallaecimonas mangrovi	78.9138	355	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820085.1	s__Aeromonas sanarellii	78.2469	316	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_900637545.1	s__Aeromonas encheleia	78.0351	320	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_000819865.1	s__Aeromonas eucrenophila	77.9647	287	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016746085.1	s__CGMCC-1-18722 sp016746085	77.9088	338	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__CGMCC-1-18722	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820165.1	s__Aeromonas taiwanensis	77.8931	326	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000820125.1	s__Aeromonas simiae	77.8667	248	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.54	0.89	0.89	2	-
GCF_000819765.1	s__Aeromonas bivalvium	77.8323	319	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_000148645.1	s__Ferrimonas balearica	77.8277	213	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819805.1	s__Aeromonas diversa	77.7342	275	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000820105.1	s__Aeromonas schubertii	77.7325	279	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.15	98.66	0.97	0.94	4	-
GCF_000820305.1	s__Aeromonas dhakensis	77.6627	305	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_005116715.1	s__Ferrimonas sp005116715	77.5026	286	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	77.1337	234	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	77.1149	232	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	76.9447	224	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011742915.1	s__Halomonas desiderata	76.8099	175	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:03,495] [INFO] GTDB search result was written to GCF_030450055.1_ASM3045005v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:03,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:03,501] [INFO] DFAST_QC result json was written to GCF_030450055.1_ASM3045005v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:03,501] [INFO] DFAST_QC completed!
[2024-01-24 13:34:03,502] [INFO] Total running time: 0h1m33s