[2023-06-28 00:03:35,047] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:03:35,049] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:03:35,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg06dbdc21-636d-47bb-872b-2e8dd0d1739c/dqc_reference
[2023-06-28 00:03:36,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:03:36,363] [INFO] Task started: Prodigal
[2023-06-28 00:03:36,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a69f057-d13a-455c-b52a-5250defcc29b/GCA_026400425.1_ASM2640042v1_genomic.fna.gz | prodigal -d GCA_026400425.1_ASM2640042v1_genomic.fna/cds.fna -a GCA_026400425.1_ASM2640042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:03:49,051] [INFO] Task succeeded: Prodigal
[2023-06-28 00:03:49,051] [INFO] Task started: HMMsearch
[2023-06-28 00:03:49,051] [INFO] Running command: hmmsearch --tblout GCA_026400425.1_ASM2640042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06dbdc21-636d-47bb-872b-2e8dd0d1739c/dqc_reference/reference_markers.hmm GCA_026400425.1_ASM2640042v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:03:49,351] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:03:49,352] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8a69f057-d13a-455c-b52a-5250defcc29b/GCA_026400425.1_ASM2640042v1_genomic.fna.gz]
[2023-06-28 00:03:49,408] [INFO] Query marker FASTA was written to GCA_026400425.1_ASM2640042v1_genomic.fna/markers.fasta
[2023-06-28 00:03:49,408] [INFO] Task started: Blastn
[2023-06-28 00:03:49,408] [INFO] Running command: blastn -query GCA_026400425.1_ASM2640042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06dbdc21-636d-47bb-872b-2e8dd0d1739c/dqc_reference/reference_markers.fasta -out GCA_026400425.1_ASM2640042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:03:50,274] [INFO] Task succeeded: Blastn
[2023-06-28 00:03:50,278] [INFO] Selected 24 target genomes.
[2023-06-28 00:03:50,278] [INFO] Target genome list was writen to GCA_026400425.1_ASM2640042v1_genomic.fna/target_genomes.txt
[2023-06-28 00:03:50,281] [INFO] Task started: fastANI
[2023-06-28 00:03:50,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a69f057-d13a-455c-b52a-5250defcc29b/GCA_026400425.1_ASM2640042v1_genomic.fna.gz --refList GCA_026400425.1_ASM2640042v1_genomic.fna/target_genomes.txt --output GCA_026400425.1_ASM2640042v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:04:25,372] [INFO] Task succeeded: fastANI
[2023-06-28 00:04:25,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06dbdc21-636d-47bb-872b-2e8dd0d1739c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:04:25,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06dbdc21-636d-47bb-872b-2e8dd0d1739c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:04:25,400] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:04:25,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:04:25,400] [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
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	79.8551	559	1273	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	79.6976	621	1273	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	79.5857	581	1273	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	79.5795	583	1273	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	79.5735	589	1273	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	79.5725	650	1273	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	79.5648	636	1273	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	79.5496	660	1273	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	79.5417	636	1273	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	79.5348	580	1273	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	79.5153	681	1273	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	79.5073	667	1273	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	79.5026	692	1273	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	79.488	614	1273	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	79.4862	633	1273	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	79.4595	633	1273	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	79.3909	611	1273	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	79.3392	654	1273	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	79.3224	655	1273	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	79.3072	643	1273	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	79.2394	446	1273	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	79.1879	582	1273	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	79.1072	469	1273	95	below_threshold
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	78.9087	465	1273	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:04:25,403] [INFO] DFAST Taxonomy check result was written to GCA_026400425.1_ASM2640042v1_genomic.fna/tc_result.tsv
[2023-06-28 00:04:25,403] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:04:25,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:04:25,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06dbdc21-636d-47bb-872b-2e8dd0d1739c/dqc_reference/checkm_data
[2023-06-28 00:04:25,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:04:25,453] [INFO] Task started: CheckM
[2023-06-28 00:04:25,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400425.1_ASM2640042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400425.1_ASM2640042v1_genomic.fna/checkm_input GCA_026400425.1_ASM2640042v1_genomic.fna/checkm_result
[2023-06-28 00:05:06,718] [INFO] Task succeeded: CheckM
[2023-06-28 00:05:06,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.84%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:05:06,762] [INFO] ===== Completeness check finished =====
[2023-06-28 00:05:06,762] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:05:06,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400425.1_ASM2640042v1_genomic.fna/markers.fasta)
[2023-06-28 00:05:06,762] [INFO] Task started: Blastn
[2023-06-28 00:05:06,763] [INFO] Running command: blastn -query GCA_026400425.1_ASM2640042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06dbdc21-636d-47bb-872b-2e8dd0d1739c/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400425.1_ASM2640042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:05:08,322] [INFO] Task succeeded: Blastn
[2023-06-28 00:05:08,329] [INFO] Selected 8 target genomes.
[2023-06-28 00:05:08,329] [INFO] Target genome list was writen to GCA_026400425.1_ASM2640042v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:05:08,338] [INFO] Task started: fastANI
[2023-06-28 00:05:08,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a69f057-d13a-455c-b52a-5250defcc29b/GCA_026400425.1_ASM2640042v1_genomic.fna.gz --refList GCA_026400425.1_ASM2640042v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400425.1_ASM2640042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:05:18,470] [INFO] Task succeeded: fastANI
[2023-06-28 00:05:18,479] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:05:18,479] [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
GCA_004173095.1	s__Tardiphaga sp004173095	91.22	859	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018279705.1	s__Tardiphaga sp018279705	84.7659	951	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256345.1	s__Tardiphaga sp002256345	84.7394	988	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359755.1	s__Tardiphaga robiniae	82.4225	885	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	96.54	96.42	0.88	0.87	5	-
GCF_001618955.1	s__Tardiphaga robiniae_A	82.2772	877	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096755.1	s__Tardiphaga sp003096755	82.2381	890	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114605.1	s__Tardiphaga sp900114605	82.2151	897	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	98.23	98.23	0.94	0.94	2	-
GCF_008329525.1	s__Tardiphaga sp008329525	82.1416	884	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:05:18,482] [INFO] GTDB search result was written to GCA_026400425.1_ASM2640042v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:05:18,485] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:05:18,490] [INFO] DFAST_QC result json was written to GCA_026400425.1_ASM2640042v1_genomic.fna/dqc_result.json
[2023-06-28 00:05:18,490] [INFO] DFAST_QC completed!
[2023-06-28 00:05:18,490] [INFO] Total running time: 0h1m43s