[2023-06-30 03:48:44,722] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:48:44,730] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:48:44,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg70f1e05c-0d13-4cf8-931a-a1170ed38db7/dqc_reference
[2023-06-30 03:48:45,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:48:45,946] [INFO] Task started: Prodigal
[2023-06-30 03:48:45,947] [INFO] Running command: gunzip -c /var/lib/cwl/stgaed03393-bacd-441b-a8a5-d8e5469e8c1a/GCA_025698885.1_ASM2569888v1_genomic.fna.gz | prodigal -d GCA_025698885.1_ASM2569888v1_genomic.fna/cds.fna -a GCA_025698885.1_ASM2569888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:48:56,268] [INFO] Task succeeded: Prodigal
[2023-06-30 03:48:56,268] [INFO] Task started: HMMsearch
[2023-06-30 03:48:56,268] [INFO] Running command: hmmsearch --tblout GCA_025698885.1_ASM2569888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70f1e05c-0d13-4cf8-931a-a1170ed38db7/dqc_reference/reference_markers.hmm GCA_025698885.1_ASM2569888v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:48:56,528] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:48:56,530] [INFO] Found 6/6 markers.
[2023-06-30 03:48:56,564] [INFO] Query marker FASTA was written to GCA_025698885.1_ASM2569888v1_genomic.fna/markers.fasta
[2023-06-30 03:48:56,565] [INFO] Task started: Blastn
[2023-06-30 03:48:56,565] [INFO] Running command: blastn -query GCA_025698885.1_ASM2569888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70f1e05c-0d13-4cf8-931a-a1170ed38db7/dqc_reference/reference_markers.fasta -out GCA_025698885.1_ASM2569888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:48:57,407] [INFO] Task succeeded: Blastn
[2023-06-30 03:48:57,410] [INFO] Selected 23 target genomes.
[2023-06-30 03:48:57,411] [INFO] Target genome list was writen to GCA_025698885.1_ASM2569888v1_genomic.fna/target_genomes.txt
[2023-06-30 03:48:57,412] [INFO] Task started: fastANI
[2023-06-30 03:48:57,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgaed03393-bacd-441b-a8a5-d8e5469e8c1a/GCA_025698885.1_ASM2569888v1_genomic.fna.gz --refList GCA_025698885.1_ASM2569888v1_genomic.fna/target_genomes.txt --output GCA_025698885.1_ASM2569888v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:49:25,993] [INFO] Task succeeded: fastANI
[2023-06-30 03:49:25,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70f1e05c-0d13-4cf8-931a-a1170ed38db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:49:25,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70f1e05c-0d13-4cf8-931a-a1170ed38db7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:49:26,012] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:49:26,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:49:26,013] [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
Nitrobacter winogradskyi	strain=Nb-255	GCA_000012725.1	913	913	type	True	87.5175	879	1176	95	below_threshold
Nitrobacter hamburgensis	strain=X14	GCA_000013885.1	912	912	type	True	84.6227	825	1176	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	79.4137	495	1176	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	79.3229	478	1176	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.2566	457	1176	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	79.1852	488	1176	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	79.1838	476	1176	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	79.1635	488	1176	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	79.1252	454	1176	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	79.0934	498	1176	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	79.0871	461	1176	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	79.069	455	1176	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	79.002	469	1176	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	78.9948	479	1176	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	78.9572	473	1176	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	78.9494	446	1176	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	78.9029	448	1176	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	78.8652	463	1176	95	below_threshold
Bradyrhizobium archetypum	strain=WSM 1744	GCA_013114835.1	2721160	2721160	type	True	78.764	479	1176	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	78.5009	378	1176	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	76.5158	66	1176	95	below_threshold
Novosphingobium hassiacum	strain=DSM 14552	GCA_014196055.1	173676	173676	type	True	76.333	63	1176	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	76.2574	60	1176	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:49:26,015] [INFO] DFAST Taxonomy check result was written to GCA_025698885.1_ASM2569888v1_genomic.fna/tc_result.tsv
[2023-06-30 03:49:26,016] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:49:26,016] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:49:26,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70f1e05c-0d13-4cf8-931a-a1170ed38db7/dqc_reference/checkm_data
[2023-06-30 03:49:26,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:49:26,058] [INFO] Task started: CheckM
[2023-06-30 03:49:26,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025698885.1_ASM2569888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025698885.1_ASM2569888v1_genomic.fna/checkm_input GCA_025698885.1_ASM2569888v1_genomic.fna/checkm_result
[2023-06-30 03:50:00,635] [INFO] Task succeeded: CheckM
[2023-06-30 03:50:00,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:50:00,662] [INFO] ===== Completeness check finished =====
[2023-06-30 03:50:00,662] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:50:00,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025698885.1_ASM2569888v1_genomic.fna/markers.fasta)
[2023-06-30 03:50:00,663] [INFO] Task started: Blastn
[2023-06-30 03:50:00,663] [INFO] Running command: blastn -query GCA_025698885.1_ASM2569888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70f1e05c-0d13-4cf8-931a-a1170ed38db7/dqc_reference/reference_markers_gtdb.fasta -out GCA_025698885.1_ASM2569888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:50:02,047] [INFO] Task succeeded: Blastn
[2023-06-30 03:50:02,051] [INFO] Selected 10 target genomes.
[2023-06-30 03:50:02,052] [INFO] Target genome list was writen to GCA_025698885.1_ASM2569888v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:50:02,057] [INFO] Task started: fastANI
[2023-06-30 03:50:02,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgaed03393-bacd-441b-a8a5-d8e5469e8c1a/GCA_025698885.1_ASM2569888v1_genomic.fna.gz --refList GCA_025698885.1_ASM2569888v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025698885.1_ASM2569888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:50:11,339] [INFO] Task succeeded: fastANI
[2023-06-30 03:50:11,352] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:50:11,352] [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_000152905.1	s__Nitrobacter sp000152905	99.2458	1041	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002028545.1	s__Nitrobacter vulgaris	88.3464	895	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539545.1	s__Nitrobacter winogradskyi_A	87.7941	824	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012725.1	s__Nitrobacter winogradskyi	87.5085	880	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013885.1	s__Nitrobacter hamburgensis	84.6383	824	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897285.1	s__Nitrobacter sp001897285	83.3604	731	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_001896955.1	s__Nitrobacter sp001896955	83.113	711	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305665.1	s__Nitrobacter sp017305665	80.6803	622	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:50:11,355] [INFO] GTDB search result was written to GCA_025698885.1_ASM2569888v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:50:11,355] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:50:11,360] [INFO] DFAST_QC result json was written to GCA_025698885.1_ASM2569888v1_genomic.fna/dqc_result.json
[2023-06-30 03:50:11,360] [INFO] DFAST_QC completed!
[2023-06-30 03:50:11,360] [INFO] Total running time: 0h1m27s