[2024-01-24 13:37:27,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd231d41-cd19-46ed-85c6-aea67a0f20c0/dqc_reference
[2024-01-24 13:37:28,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:28,997] [INFO] Task started: Prodigal
[2024-01-24 13:37:28,997] [INFO] Running command: gunzip -c /var/lib/cwl/stgdca87f0f-cc92-4b76-8452-cf91a3c2ca3a/GCF_014534685.1_ASM1453468v1_genomic.fna.gz | prodigal -d GCF_014534685.1_ASM1453468v1_genomic.fna/cds.fna -a GCF_014534685.1_ASM1453468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:43,986] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:43,987] [INFO] Task started: HMMsearch
[2024-01-24 13:37:43,987] [INFO] Running command: hmmsearch --tblout GCF_014534685.1_ASM1453468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd231d41-cd19-46ed-85c6-aea67a0f20c0/dqc_reference/reference_markers.hmm GCF_014534685.1_ASM1453468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:44,292] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:44,293] [INFO] Found 6/6 markers.
[2024-01-24 13:37:44,336] [INFO] Query marker FASTA was written to GCF_014534685.1_ASM1453468v1_genomic.fna/markers.fasta
[2024-01-24 13:37:44,336] [INFO] Task started: Blastn
[2024-01-24 13:37:44,336] [INFO] Running command: blastn -query GCF_014534685.1_ASM1453468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd231d41-cd19-46ed-85c6-aea67a0f20c0/dqc_reference/reference_markers.fasta -out GCF_014534685.1_ASM1453468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:45,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:45,255] [INFO] Selected 22 target genomes.
[2024-01-24 13:37:45,255] [INFO] Target genome list was writen to GCF_014534685.1_ASM1453468v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:45,269] [INFO] Task started: fastANI
[2024-01-24 13:37:45,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca87f0f-cc92-4b76-8452-cf91a3c2ca3a/GCF_014534685.1_ASM1453468v1_genomic.fna.gz --refList GCF_014534685.1_ASM1453468v1_genomic.fna/target_genomes.txt --output GCF_014534685.1_ASM1453468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:09,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:09,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd231d41-cd19-46ed-85c6-aea67a0f20c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:09,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd231d41-cd19-46ed-85c6-aea67a0f20c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:09,981] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:38:09,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:38:09,982] [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
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	80.5562	698	1614	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	80.4933	680	1614	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	80.4267	710	1614	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	80.4249	692	1614	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	80.4125	710	1614	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	80.3398	694	1614	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	80.218	693	1614	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	80.1049	686	1614	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	79.9309	639	1614	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	79.8744	693	1614	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	79.8466	667	1614	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	79.8439	673	1614	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	79.8181	670	1614	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	79.7677	647	1614	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	79.7433	661	1614	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.7323	671	1614	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	79.702	635	1614	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.6867	640	1614	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	79.6213	604	1614	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.948	583	1614	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.4087	466	1614	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.4045	466	1614	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:09,983] [INFO] DFAST Taxonomy check result was written to GCF_014534685.1_ASM1453468v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:09,984] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:09,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:09,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd231d41-cd19-46ed-85c6-aea67a0f20c0/dqc_reference/checkm_data
[2024-01-24 13:38:09,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:10,036] [INFO] Task started: CheckM
[2024-01-24 13:38:10,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014534685.1_ASM1453468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014534685.1_ASM1453468v1_genomic.fna/checkm_input GCF_014534685.1_ASM1453468v1_genomic.fna/checkm_result
[2024-01-24 13:38:54,741] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:54,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:54,767] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:54,767] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:54,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014534685.1_ASM1453468v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:54,768] [INFO] Task started: Blastn
[2024-01-24 13:38:54,769] [INFO] Running command: blastn -query GCF_014534685.1_ASM1453468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd231d41-cd19-46ed-85c6-aea67a0f20c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014534685.1_ASM1453468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:56,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:56,432] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:56,432] [INFO] Target genome list was writen to GCF_014534685.1_ASM1453468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:56,738] [INFO] Task started: fastANI
[2024-01-24 13:38:56,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca87f0f-cc92-4b76-8452-cf91a3c2ca3a/GCF_014534685.1_ASM1453468v1_genomic.fna.gz --refList GCF_014534685.1_ASM1453468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014534685.1_ASM1453468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:18,981] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:19,001] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:19,001] [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_014534685.1	s__Aminobacter sp014534685	100.0	1610	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014206975.1	s__Aminobacter aganoensis	80.5778	694	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCF_018555685.1	s__Aminobacter anthyllidis	80.478	694	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200015.1	s__Aminobacter niigataensis	80.4674	683	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_900445235.1	s__Aminobacter aminovorans	80.4264	691	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014138625.1	s__Aminobacter ciceronei	80.3965	713	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.84	97.89	0.89	0.85	7	-
GCF_014863355.1	s__Aminobacter carboxidus	80.3668	710	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.38	98.38	0.89	0.89	2	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	80.1232	666	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_003148805.1	s__Aminobacter sp003148805	80.1033	646	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	79.9539	681	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_000427725.1	s__Mesorhizobium sp000427725	79.8821	653	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016836705.1	s__Mesorhizobium caraganae	79.8456	668	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCF_003601975.1	s__Mesorhizobium waimense	79.8365	674	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688075.1	s__Mesorhizobium sp000688075	79.8117	700	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002270415.1	s__Mesorhizobium sophorae	79.8004	673	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513935.1	s__Mesorhizobium sp000513935	79.7831	637	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.65	0.86	0.84	7	-
GCF_018588885.1	s__Mesorhizobium sp018588885	79.7101	664	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439515.1	s__Mesorhizobium sp006439515	79.5542	665	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.05	0.91	0.91	2	-
GCA_002336975.1	s__Mesorhizobium_A sp002336975	79.0143	382	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842935.1	s__DUSC01 sp012842935	78.7391	435	1614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:19,003] [INFO] GTDB search result was written to GCF_014534685.1_ASM1453468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:19,004] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:19,008] [INFO] DFAST_QC result json was written to GCF_014534685.1_ASM1453468v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:19,008] [INFO] DFAST_QC completed!
[2024-01-24 13:39:19,008] [INFO] Total running time: 0h1m51s