[2024-01-24 14:05:48,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:48,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:48,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a2409ec-8aaf-4168-b43b-2ad0513484be/dqc_reference
[2024-01-24 14:05:49,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:49,915] [INFO] Task started: Prodigal
[2024-01-24 14:05:49,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg8969abe4-153a-4d1a-9c57-ec99aa02928a/GCF_005144885.1_ASM514488v1_genomic.fna.gz | prodigal -d GCF_005144885.1_ASM514488v1_genomic.fna/cds.fna -a GCF_005144885.1_ASM514488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:11,942] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:11,942] [INFO] Task started: HMMsearch
[2024-01-24 14:06:11,942] [INFO] Running command: hmmsearch --tblout GCF_005144885.1_ASM514488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a2409ec-8aaf-4168-b43b-2ad0513484be/dqc_reference/reference_markers.hmm GCF_005144885.1_ASM514488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:12,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:12,330] [INFO] Found 6/6 markers.
[2024-01-24 14:06:12,394] [INFO] Query marker FASTA was written to GCF_005144885.1_ASM514488v1_genomic.fna/markers.fasta
[2024-01-24 14:06:12,394] [INFO] Task started: Blastn
[2024-01-24 14:06:12,394] [INFO] Running command: blastn -query GCF_005144885.1_ASM514488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a2409ec-8aaf-4168-b43b-2ad0513484be/dqc_reference/reference_markers.fasta -out GCF_005144885.1_ASM514488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:13,529] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:13,532] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:13,533] [INFO] Target genome list was writen to GCF_005144885.1_ASM514488v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:13,541] [INFO] Task started: fastANI
[2024-01-24 14:06:13,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg8969abe4-153a-4d1a-9c57-ec99aa02928a/GCF_005144885.1_ASM514488v1_genomic.fna.gz --refList GCF_005144885.1_ASM514488v1_genomic.fna/target_genomes.txt --output GCF_005144885.1_ASM514488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:43,493] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:43,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a2409ec-8aaf-4168-b43b-2ad0513484be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:43,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a2409ec-8aaf-4168-b43b-2ad0513484be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:43,512] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:43,512] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:43,512] [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
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	100.0	2449	2451	95	conclusive
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	80.8423	975	2451	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	80.7102	1005	2451	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	77.9246	711	2451	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.7035	448	2451	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.5563	496	2451	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.5505	547	2451	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.4311	539	2451	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.4279	352	2451	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	77.3716	600	2451	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	77.3589	566	2451	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.3297	437	2451	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.293	595	2451	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	77.2206	630	2451	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.2035	377	2451	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.1973	395	2451	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.1568	642	2451	95	below_threshold
Microvirga pudoricolor	strain=BT291	GCA_016892705.1	2778729	2778729	type	True	77.1467	305	2451	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	77.138	504	2451	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.109	498	2451	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	77.0554	620	2451	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	77.0531	575	2451	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	76.9138	413	2451	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.7106	575	2451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:43,514] [INFO] DFAST Taxonomy check result was written to GCF_005144885.1_ASM514488v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:43,514] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:43,514] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:43,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a2409ec-8aaf-4168-b43b-2ad0513484be/dqc_reference/checkm_data
[2024-01-24 14:06:43,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:43,584] [INFO] Task started: CheckM
[2024-01-24 14:06:43,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005144885.1_ASM514488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005144885.1_ASM514488v1_genomic.fna/checkm_input GCF_005144885.1_ASM514488v1_genomic.fna/checkm_result
[2024-01-24 14:08:15,790] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:15,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:15,812] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:15,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:15,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005144885.1_ASM514488v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:15,813] [INFO] Task started: Blastn
[2024-01-24 14:08:15,814] [INFO] Running command: blastn -query GCF_005144885.1_ASM514488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a2409ec-8aaf-4168-b43b-2ad0513484be/dqc_reference/reference_markers_gtdb.fasta -out GCF_005144885.1_ASM514488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:18,160] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:18,163] [INFO] Selected 8 target genomes.
[2024-01-24 14:08:18,163] [INFO] Target genome list was writen to GCF_005144885.1_ASM514488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:18,170] [INFO] Task started: fastANI
[2024-01-24 14:08:18,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg8969abe4-153a-4d1a-9c57-ec99aa02928a/GCF_005144885.1_ASM514488v1_genomic.fna.gz --refList GCF_005144885.1_ASM514488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005144885.1_ASM514488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:32,195] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:32,203] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:32,203] [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_005144885.1	s__Phreatobacter stygius	100.0	2451	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017304475.1	s__Phreatobacter sp017304475	87.5543	1977	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000751295.2	s__Phreatobacter sp000751295	83.8611	1605	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005160265.1	s__Phreatobacter sp005160265	81.5892	1058	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793595.1	s__Phreatobacter sp016793595	81.1788	1046	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046185.1	s__Phreatobacter oligotrophus	80.8194	978	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008515.1	s__Phreatobacter cathodiphilus	80.7031	1004	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	80.5962	842	2451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:32,204] [INFO] GTDB search result was written to GCF_005144885.1_ASM514488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:32,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:32,208] [INFO] DFAST_QC result json was written to GCF_005144885.1_ASM514488v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:32,208] [INFO] DFAST_QC completed!
[2024-01-24 14:08:32,209] [INFO] Total running time: 0h2m44s