[2024-01-24 13:49:55,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f0d12d8-e303-445b-b791-f127402cac26/dqc_reference
[2024-01-24 13:49:56,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,742] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bf4809f-cc06-4921-ba6b-062af60a9a4b/GCF_019793435.1_ASM1979343v1_genomic.fna.gz | prodigal -d GCF_019793435.1_ASM1979343v1_genomic.fna/cds.fna -a GCF_019793435.1_ASM1979343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:17,791] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:17,791] [INFO] Task started: HMMsearch
[2024-01-24 13:50:17,791] [INFO] Running command: hmmsearch --tblout GCF_019793435.1_ASM1979343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f0d12d8-e303-445b-b791-f127402cac26/dqc_reference/reference_markers.hmm GCF_019793435.1_ASM1979343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:18,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:18,130] [INFO] Found 6/6 markers.
[2024-01-24 13:50:18,189] [INFO] Query marker FASTA was written to GCF_019793435.1_ASM1979343v1_genomic.fna/markers.fasta
[2024-01-24 13:50:18,190] [INFO] Task started: Blastn
[2024-01-24 13:50:18,190] [INFO] Running command: blastn -query GCF_019793435.1_ASM1979343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f0d12d8-e303-445b-b791-f127402cac26/dqc_reference/reference_markers.fasta -out GCF_019793435.1_ASM1979343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:19,215] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:19,218] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:19,218] [INFO] Target genome list was writen to GCF_019793435.1_ASM1979343v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:19,222] [INFO] Task started: fastANI
[2024-01-24 13:50:19,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf4809f-cc06-4921-ba6b-062af60a9a4b/GCF_019793435.1_ASM1979343v1_genomic.fna.gz --refList GCF_019793435.1_ASM1979343v1_genomic.fna/target_genomes.txt --output GCF_019793435.1_ASM1979343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:45,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f0d12d8-e303-445b-b791-f127402cac26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:45,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f0d12d8-e303-445b-b791-f127402cac26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:45,058] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:45,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:45,059] [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
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	100.0	2293	2295	95	conclusive
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	92.5525	1755	2295	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002914525.1	1538159	1538159	type	True	90.8891	1840	2295	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	90.8816	1841	2295	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	89.7892	1723	2295	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	89.2215	1729	2295	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	89.1785	1629	2295	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	89.1603	1741	2295	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	89.1249	1756	2295	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	89.086	1691	2295	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	88.9713	1724	2295	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	87.9161	1671	2295	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	87.8745	1629	2295	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.4766	1127	2295	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.4707	985	2295	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.2884	755	2295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,060] [INFO] DFAST Taxonomy check result was written to GCF_019793435.1_ASM1979343v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:45,061] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:45,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:45,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f0d12d8-e303-445b-b791-f127402cac26/dqc_reference/checkm_data
[2024-01-24 13:50:45,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:45,130] [INFO] Task started: CheckM
[2024-01-24 13:50:45,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019793435.1_ASM1979343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019793435.1_ASM1979343v1_genomic.fna/checkm_input GCF_019793435.1_ASM1979343v1_genomic.fna/checkm_result
[2024-01-24 13:51:41,783] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:41,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:41,810] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:41,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:41,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019793435.1_ASM1979343v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:41,811] [INFO] Task started: Blastn
[2024-01-24 13:51:41,811] [INFO] Running command: blastn -query GCF_019793435.1_ASM1979343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f0d12d8-e303-445b-b791-f127402cac26/dqc_reference/reference_markers_gtdb.fasta -out GCF_019793435.1_ASM1979343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:43,791] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:43,796] [INFO] Selected 12 target genomes.
[2024-01-24 13:51:43,796] [INFO] Target genome list was writen to GCF_019793435.1_ASM1979343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:43,826] [INFO] Task started: fastANI
[2024-01-24 13:51:43,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf4809f-cc06-4921-ba6b-062af60a9a4b/GCF_019793435.1_ASM1979343v1_genomic.fna.gz --refList GCF_019793435.1_ASM1979343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019793435.1_ASM1979343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:05,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:05,088] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:05,089] [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_002531905.1	s__Rhizobium sp002531905	99.5061	2108	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.24	98.93	0.89	0.86	4	conclusive
GCF_002531755.2	s__Rhizobium acidisoli	93.9364	1952	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.40	0.88	0.80	8	-
GCF_001664485.1	s__Rhizobium sp001664485	92.6348	1881	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_001187535.1	s__Rhizobium ecuadorense	92.55	1756	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.31	0.89	0.89	4	-
GCF_010668805.1	s__Rhizobium phaseoli_A	90.9687	1764	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	90.6398	1801	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876795.1	s__Rhizobium leguminosarum_P	90.534	1768	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292525.1	s__Rhizobium sp000292525	90.4433	1776	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357385.1	s__Rhizobium sp017357385	90.371	1787	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531725.1	s__Rhizobium sp002531725	89.9058	1835	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003939025.1	s__Rhizobium sophoriradicis	89.0847	1691	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	97.30	0.92	0.88	16	-
GCF_003938655.1	s__Rhizobium pisi	87.8908	1627	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.78	97.55	0.94	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:05,091] [INFO] GTDB search result was written to GCF_019793435.1_ASM1979343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:05,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:05,095] [INFO] DFAST_QC result json was written to GCF_019793435.1_ASM1979343v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:05,096] [INFO] DFAST_QC completed!
[2024-01-24 13:52:05,096] [INFO] Total running time: 0h2m10s