[2023-06-04 17:34:42,658] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:34:42,661] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:34:42,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg30613669-3c33-4dbf-990b-aed9603b1823/dqc_reference
[2023-06-04 17:34:43,970] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:34:43,971] [INFO] Task started: Prodigal
[2023-06-04 17:34:43,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg0369b249-0d14-4714-b7e5-bd24e2450a9e/GCA_004018025.1_ASM401802v1_genomic.fna.gz | prodigal -d GCA_004018025.1_ASM401802v1_genomic.fna/cds.fna -a GCA_004018025.1_ASM401802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:35:04,647] [INFO] Task succeeded: Prodigal
[2023-06-04 17:35:04,648] [INFO] Task started: HMMsearch
[2023-06-04 17:35:04,648] [INFO] Running command: hmmsearch --tblout GCA_004018025.1_ASM401802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30613669-3c33-4dbf-990b-aed9603b1823/dqc_reference/reference_markers.hmm GCA_004018025.1_ASM401802v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:35:05,003] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:35:05,004] [INFO] Found 6/6 markers.
[2023-06-04 17:35:05,062] [INFO] Query marker FASTA was written to GCA_004018025.1_ASM401802v1_genomic.fna/markers.fasta
[2023-06-04 17:35:05,062] [INFO] Task started: Blastn
[2023-06-04 17:35:05,062] [INFO] Running command: blastn -query GCA_004018025.1_ASM401802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30613669-3c33-4dbf-990b-aed9603b1823/dqc_reference/reference_markers.fasta -out GCA_004018025.1_ASM401802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:35:06,340] [INFO] Task succeeded: Blastn
[2023-06-04 17:35:06,346] [INFO] Selected 19 target genomes.
[2023-06-04 17:35:06,347] [INFO] Target genome list was writen to GCA_004018025.1_ASM401802v1_genomic.fna/target_genomes.txt
[2023-06-04 17:35:06,584] [INFO] Task started: fastANI
[2023-06-04 17:35:06,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg0369b249-0d14-4714-b7e5-bd24e2450a9e/GCA_004018025.1_ASM401802v1_genomic.fna.gz --refList GCA_004018025.1_ASM401802v1_genomic.fna/target_genomes.txt --output GCA_004018025.1_ASM401802v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:35:38,827] [INFO] Task succeeded: fastANI
[2023-06-04 17:35:38,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30613669-3c33-4dbf-990b-aed9603b1823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:35:38,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30613669-3c33-4dbf-990b-aed9603b1823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:35:38,844] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:35:38,844] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:35:38,844] [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 australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	90.9967	1639	2193	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	88.592	1621	2193	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	88.4371	1678	2193	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	88.395	1694	2193	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	88.2593	1735	2193	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	88.1998	1649	2193	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	87.9433	1509	2193	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	87.8917	1683	2193	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	87.3219	1654	2193	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.3077	1596	2193	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	87.1073	1640	2193	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	86.9118	1618	2193	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	86.7396	1620	2193	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	85.4822	1494	2193	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	85.3603	1465	2193	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.395	1334	2193	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.1749	689	2193	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.1737	690	2193	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.8307	621	2193	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:35:38,851] [INFO] DFAST Taxonomy check result was written to GCA_004018025.1_ASM401802v1_genomic.fna/tc_result.tsv
[2023-06-04 17:35:38,852] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:35:38,852] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:35:38,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30613669-3c33-4dbf-990b-aed9603b1823/dqc_reference/checkm_data
[2023-06-04 17:35:38,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:35:38,925] [INFO] Task started: CheckM
[2023-06-04 17:35:38,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004018025.1_ASM401802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004018025.1_ASM401802v1_genomic.fna/checkm_input GCA_004018025.1_ASM401802v1_genomic.fna/checkm_result
[2023-06-04 17:36:37,650] [INFO] Task succeeded: CheckM
[2023-06-04 17:36:37,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:36:37,685] [INFO] ===== Completeness check finished =====
[2023-06-04 17:36:37,685] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:36:37,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004018025.1_ASM401802v1_genomic.fna/markers.fasta)
[2023-06-04 17:36:37,686] [INFO] Task started: Blastn
[2023-06-04 17:36:37,686] [INFO] Running command: blastn -query GCA_004018025.1_ASM401802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30613669-3c33-4dbf-990b-aed9603b1823/dqc_reference/reference_markers_gtdb.fasta -out GCA_004018025.1_ASM401802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:36:39,841] [INFO] Task succeeded: Blastn
[2023-06-04 17:36:39,847] [INFO] Selected 9 target genomes.
[2023-06-04 17:36:39,847] [INFO] Target genome list was writen to GCA_004018025.1_ASM401802v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:36:40,095] [INFO] Task started: fastANI
[2023-06-04 17:36:40,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg0369b249-0d14-4714-b7e5-bd24e2450a9e/GCA_004018025.1_ASM401802v1_genomic.fna.gz --refList GCA_004018025.1_ASM401802v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004018025.1_ASM401802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:36:56,414] [INFO] Task succeeded: fastANI
[2023-06-04 17:36:56,424] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:36:56,424] [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_004791165.1	s__Mesorhizobium sp004791165	95.9609	1947	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.22	95.93	0.90	0.87	21	conclusive
GCF_006439515.1	s__Mesorhizobium sp006439515	92.1517	1624	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.05	0.91	0.91	2	-
GCF_000513935.1	s__Mesorhizobium sp000513935	92.0625	1592	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.65	0.86	0.84	7	-
GCF_008520305.1	s__Mesorhizobium sp008520305	91.951	1632	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442205.1	s__Mesorhizobium sp006442205	91.5346	1663	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230995.2	s__Mesorhizobium australicum	91.0067	1638	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.45	95.19	0.87	0.83	12	-
GCF_006442315.1	s__Mesorhizobium sp006442315	89.5633	1639	2193	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	88.282	1732	2193	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	86.1707	1515	2193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:36:56,427] [INFO] GTDB search result was written to GCA_004018025.1_ASM401802v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:36:56,427] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:36:56,433] [INFO] DFAST_QC result json was written to GCA_004018025.1_ASM401802v1_genomic.fna/dqc_result.json
[2023-06-04 17:36:56,433] [INFO] DFAST_QC completed!
[2023-06-04 17:36:56,433] [INFO] Total running time: 0h2m14s