[2024-01-25 20:27:20,786] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg70ca3540-ff02-4501-9864-061efc588d38/dqc_reference
[2024-01-25 20:27:21,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:21,936] [INFO] Task started: Prodigal
[2024-01-25 20:27:21,936] [INFO] Running command: gunzip -c /var/lib/cwl/stgc25e14d9-edd7-4e48-af7d-d5aa0927539b/GCF_015690355.1_ASM1569035v1_genomic.fna.gz | prodigal -d GCF_015690355.1_ASM1569035v1_genomic.fna/cds.fna -a GCF_015690355.1_ASM1569035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:42,627] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:42,627] [INFO] Task started: HMMsearch
[2024-01-25 20:27:42,627] [INFO] Running command: hmmsearch --tblout GCF_015690355.1_ASM1569035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70ca3540-ff02-4501-9864-061efc588d38/dqc_reference/reference_markers.hmm GCF_015690355.1_ASM1569035v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:42,943] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:42,944] [INFO] Found 6/6 markers.
[2024-01-25 20:27:43,016] [INFO] Query marker FASTA was written to GCF_015690355.1_ASM1569035v1_genomic.fna/markers.fasta
[2024-01-25 20:27:43,016] [INFO] Task started: Blastn
[2024-01-25 20:27:43,017] [INFO] Running command: blastn -query GCF_015690355.1_ASM1569035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70ca3540-ff02-4501-9864-061efc588d38/dqc_reference/reference_markers.fasta -out GCF_015690355.1_ASM1569035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:44,297] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:44,301] [INFO] Selected 15 target genomes.
[2024-01-25 20:27:44,302] [INFO] Target genome list was writen to GCF_015690355.1_ASM1569035v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:44,322] [INFO] Task started: fastANI
[2024-01-25 20:27:44,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgc25e14d9-edd7-4e48-af7d-d5aa0927539b/GCF_015690355.1_ASM1569035v1_genomic.fna.gz --refList GCF_015690355.1_ASM1569035v1_genomic.fna/target_genomes.txt --output GCF_015690355.1_ASM1569035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:17,370] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:17,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70ca3540-ff02-4501-9864-061efc588d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:17,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70ca3540-ff02-4501-9864-061efc588d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:17,381] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:28:17,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:17,381] [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
Streptacidiphilus fuscans	strain=NEAU-YB345	GCA_015690355.1	2789292	2789292	type	True	100.0	2766	2840	95	conclusive
Streptacidiphilus pinicola	strain=MMS16-CNU450	GCA_003258295.1	2219663	2219663	type	True	84.875	1611	2840	95	below_threshold
Streptacidiphilus rugosus	strain=AM-16	GCA_000744655.1	405783	405783	type	True	84.6442	1637	2840	95	below_threshold
Streptacidiphilus anmyonensis	strain=NBRC 103185	GCA_000787855.1	405782	405782	type	True	84.519	1739	2840	95	below_threshold
Streptacidiphilus neutrinimicus	strain=NBRC 100921	GCA_000787815.1	105420	105420	type	True	84.4681	1643	2840	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	84.4345	1712	2840	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	84.3145	1741	2840	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	84.1953	1748	2840	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	81.562	1376	2840	95	below_threshold
Streptacidiphilus albus	strain=JL83	GCA_000744705.1	105425	105425	type	True	81.4702	1424	2840	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	79.239	922	2840	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	78.8479	890	2840	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	78.8009	941	2840	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	78.6576	1030	2840	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	78.5323	993	2840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:17,382] [INFO] DFAST Taxonomy check result was written to GCF_015690355.1_ASM1569035v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:17,383] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:17,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:17,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70ca3540-ff02-4501-9864-061efc588d38/dqc_reference/checkm_data
[2024-01-25 20:28:17,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:17,456] [INFO] Task started: CheckM
[2024-01-25 20:28:17,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015690355.1_ASM1569035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015690355.1_ASM1569035v1_genomic.fna/checkm_input GCF_015690355.1_ASM1569035v1_genomic.fna/checkm_result
[2024-01-25 20:30:07,217] [INFO] Task succeeded: CheckM
[2024-01-25 20:30:07,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 20:30:07,238] [INFO] ===== Completeness check finished =====
[2024-01-25 20:30:07,238] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:30:07,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015690355.1_ASM1569035v1_genomic.fna/markers.fasta)
[2024-01-25 20:30:07,239] [INFO] Task started: Blastn
[2024-01-25 20:30:07,239] [INFO] Running command: blastn -query GCF_015690355.1_ASM1569035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70ca3540-ff02-4501-9864-061efc588d38/dqc_reference/reference_markers_gtdb.fasta -out GCF_015690355.1_ASM1569035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:30:09,356] [INFO] Task succeeded: Blastn
[2024-01-25 20:30:09,360] [INFO] Selected 9 target genomes.
[2024-01-25 20:30:09,360] [INFO] Target genome list was writen to GCF_015690355.1_ASM1569035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:30:09,380] [INFO] Task started: fastANI
[2024-01-25 20:30:09,381] [INFO] Running command: fastANI --query /var/lib/cwl/stgc25e14d9-edd7-4e48-af7d-d5aa0927539b/GCF_015690355.1_ASM1569035v1_genomic.fna.gz --refList GCF_015690355.1_ASM1569035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015690355.1_ASM1569035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:30:30,793] [INFO] Task succeeded: fastANI
[2024-01-25 20:30:30,799] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:30:30,800] [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_015690355.1	s__Streptacidiphilus fuscans	100.0	2778	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003258295.1	s__Streptacidiphilus pinicola	84.8521	1614	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744655.1	s__Streptacidiphilus rugosus	84.6094	1643	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787855.1	s__Streptacidiphilus anmyonensis	84.4763	1747	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787815.1	s__Streptacidiphilus neutrinimicus	84.4709	1643	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787835.1	s__Streptacidiphilus melanogenes	84.4271	1713	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	84.2498	1756	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000719095.1	s__Streptacidiphilus jeojiense	81.6574	1382	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744705.1	s__Streptacidiphilus albus	81.4585	1427	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:30:30,801] [INFO] GTDB search result was written to GCF_015690355.1_ASM1569035v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:30:30,802] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:30:30,804] [INFO] DFAST_QC result json was written to GCF_015690355.1_ASM1569035v1_genomic.fna/dqc_result.json
[2024-01-25 20:30:30,805] [INFO] DFAST_QC completed!
[2024-01-25 20:30:30,805] [INFO] Total running time: 0h3m10s