[2024-01-24 13:32:34,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,883] [INFO] DQC Reference Directory: /var/lib/cwl/stga18e20d0-c0b9-4cae-b72d-e740f8757d51/dqc_reference
[2024-01-24 13:32:36,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,288] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,288] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc16a8aa-b529-4391-8b6a-7d6e8e722138/GCF_000176035.2_ASM17603v2_genomic.fna.gz | prodigal -d GCF_000176035.2_ASM17603v2_genomic.fna/cds.fna -a GCF_000176035.2_ASM17603v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:59,688] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:59,688] [INFO] Task started: HMMsearch
[2024-01-24 13:32:59,688] [INFO] Running command: hmmsearch --tblout GCF_000176035.2_ASM17603v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18e20d0-c0b9-4cae-b72d-e740f8757d51/dqc_reference/reference_markers.hmm GCF_000176035.2_ASM17603v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:00,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:00,173] [INFO] Found 6/6 markers.
[2024-01-24 13:33:00,252] [INFO] Query marker FASTA was written to GCF_000176035.2_ASM17603v2_genomic.fna/markers.fasta
[2024-01-24 13:33:00,253] [INFO] Task started: Blastn
[2024-01-24 13:33:00,253] [INFO] Running command: blastn -query GCF_000176035.2_ASM17603v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga18e20d0-c0b9-4cae-b72d-e740f8757d51/dqc_reference/reference_markers.fasta -out GCF_000176035.2_ASM17603v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:01,377] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:01,380] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:01,381] [INFO] Target genome list was writen to GCF_000176035.2_ASM17603v2_genomic.fna/target_genomes.txt
[2024-01-24 13:33:01,404] [INFO] Task started: fastANI
[2024-01-24 13:33:01,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc16a8aa-b529-4391-8b6a-7d6e8e722138/GCF_000176035.2_ASM17603v2_genomic.fna.gz --refList GCF_000176035.2_ASM17603v2_genomic.fna/target_genomes.txt --output GCF_000176035.2_ASM17603v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:36,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:36,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18e20d0-c0b9-4cae-b72d-e740f8757d51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:36,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18e20d0-c0b9-4cae-b72d-e740f8757d51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:36,058] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:36,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:36,058] [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
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	100.0	2292	2294	95	conclusive
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	89.2645	1631	2294	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	89.2143	1714	2294	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	89.1258	1704	2294	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	89.001	1668	2294	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	88.9395	1719	2294	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	88.5174	1673	2294	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	88.5075	1502	2294	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	88.0387	1706	2294	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	88.0292	1635	2294	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	87.5057	1589	2294	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	87.4965	1578	2294	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.2754	1590	2294	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	85.983	1507	2294	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.7344	1365	2294	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.8944	1366	2294	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.1846	659	2294	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.1202	711	2294	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.0367	636	2294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:36,062] [INFO] DFAST Taxonomy check result was written to GCF_000176035.2_ASM17603v2_genomic.fna/tc_result.tsv
[2024-01-24 13:33:36,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:36,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:36,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18e20d0-c0b9-4cae-b72d-e740f8757d51/dqc_reference/checkm_data
[2024-01-24 13:33:36,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:36,135] [INFO] Task started: CheckM
[2024-01-24 13:33:36,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000176035.2_ASM17603v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000176035.2_ASM17603v2_genomic.fna/checkm_input GCF_000176035.2_ASM17603v2_genomic.fna/checkm_result
[2024-01-24 13:34:42,173] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:42,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:42,200] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:42,200] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:42,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000176035.2_ASM17603v2_genomic.fna/markers.fasta)
[2024-01-24 13:34:42,201] [INFO] Task started: Blastn
[2024-01-24 13:34:42,201] [INFO] Running command: blastn -query GCF_000176035.2_ASM17603v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga18e20d0-c0b9-4cae-b72d-e740f8757d51/dqc_reference/reference_markers_gtdb.fasta -out GCF_000176035.2_ASM17603v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:44,349] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:44,354] [INFO] Selected 19 target genomes.
[2024-01-24 13:34:44,355] [INFO] Target genome list was writen to GCF_000176035.2_ASM17603v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:44,396] [INFO] Task started: fastANI
[2024-01-24 13:34:44,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc16a8aa-b529-4391-8b6a-7d6e8e722138/GCF_000176035.2_ASM17603v2_genomic.fna.gz --refList GCF_000176035.2_ASM17603v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000176035.2_ASM17603v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:19,446] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:19,468] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:19,468] [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_000176035.2	s__Mesorhizobium opportunistum	100.0	2293	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.26	95.55	0.85	0.80	10	conclusive
GCF_018588885.1	s__Mesorhizobium sp018588885	89.6756	1660	2294	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	89.4976	1728	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353565.1	s__Mesorhizobium sp003353565	89.3438	1676	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	89.1824	1729	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	89.117	1706	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467435.1	s__Mesorhizobium sp016467435	89.1082	1649	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_002356515.1	s__Mesorhizobium loti_C	89.0293	1767	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.70	98.70	0.94	0.94	2	-
GCF_002295115.1	s__Mesorhizobium sp002295115	88.9433	1703	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_013170805.1	s__Mesorhizobium sp013170805	88.7551	1695	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013170845.1	s__Mesorhizobium loti_B	88.5582	1693	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000472705.1	s__Mesorhizobium erdmanii	88.519	1673	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	97.39	0.90	0.90	3	-
GCF_000472785.1	s__Mesorhizobium loti_E	88.5127	1683	2294	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	88.0476	1566	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.65	0.86	0.84	7	-
GCF_003253745.1	s__Mesorhizobium kowhaii	87.8588	1660	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425965.1	s__Mesorhizobium sp000425965	87.668	1554	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519305.1	s__Mesorhizobium ciceri_B	87.6465	1652	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503535.1	s__Mesorhizobium sp005503535	87.2641	1591	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000502955.1	s__Mesorhizobium sp000502955	87.0165	1560	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:19,470] [INFO] GTDB search result was written to GCF_000176035.2_ASM17603v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:19,470] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:19,475] [INFO] DFAST_QC result json was written to GCF_000176035.2_ASM17603v2_genomic.fna/dqc_result.json
[2024-01-24 13:35:19,475] [INFO] DFAST_QC completed!
[2024-01-24 13:35:19,475] [INFO] Total running time: 0h2m45s