[2024-01-24 12:45:20,685] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ef39fbd-0012-41ad-8514-48fe4f1206b5/dqc_reference
[2024-01-24 12:45:21,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:21,900] [INFO] Task started: Prodigal
[2024-01-24 12:45:21,900] [INFO] Running command: gunzip -c /var/lib/cwl/stge43fed57-87ee-45f6-885e-eafd5f6921ad/GCF_016862215.1_ASM1686221v1_genomic.fna.gz | prodigal -d GCF_016862215.1_ASM1686221v1_genomic.fna/cds.fna -a GCF_016862215.1_ASM1686221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:06,387] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:06,388] [INFO] Task started: HMMsearch
[2024-01-24 12:46:06,388] [INFO] Running command: hmmsearch --tblout GCF_016862215.1_ASM1686221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ef39fbd-0012-41ad-8514-48fe4f1206b5/dqc_reference/reference_markers.hmm GCF_016862215.1_ASM1686221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:06,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:06,816] [INFO] Found 6/6 markers.
[2024-01-24 12:46:07,175] [INFO] Query marker FASTA was written to GCF_016862215.1_ASM1686221v1_genomic.fna/markers.fasta
[2024-01-24 12:46:07,175] [INFO] Task started: Blastn
[2024-01-24 12:46:07,175] [INFO] Running command: blastn -query GCF_016862215.1_ASM1686221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ef39fbd-0012-41ad-8514-48fe4f1206b5/dqc_reference/reference_markers.fasta -out GCF_016862215.1_ASM1686221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:08,330] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:08,335] [INFO] Selected 14 target genomes.
[2024-01-24 12:46:08,336] [INFO] Target genome list was writen to GCF_016862215.1_ASM1686221v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:08,356] [INFO] Task started: fastANI
[2024-01-24 12:46:08,357] [INFO] Running command: fastANI --query /var/lib/cwl/stge43fed57-87ee-45f6-885e-eafd5f6921ad/GCF_016862215.1_ASM1686221v1_genomic.fna.gz --refList GCF_016862215.1_ASM1686221v1_genomic.fna/target_genomes.txt --output GCF_016862215.1_ASM1686221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:41,060] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:41,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ef39fbd-0012-41ad-8514-48fe4f1206b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:41,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ef39fbd-0012-41ad-8514-48fe4f1206b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:41,077] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:41,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:41,077] [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
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	100.0	3606	3616	95	conclusive
Actinoplanes consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	94.7191	2986	3616	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	81.6842	1318	3616	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	81.5569	1656	3616	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	81.4923	1454	3616	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	81.4676	1680	3616	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	81.4322	1812	3616	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	79.888	1590	3616	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	79.3501	1369	3616	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	79.2046	1397	3616	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.2513	1303	3616	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.2511	1049	3616	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.2067	894	3616	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1778	1169	3616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:41,079] [INFO] DFAST Taxonomy check result was written to GCF_016862215.1_ASM1686221v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:41,079] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:41,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:41,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ef39fbd-0012-41ad-8514-48fe4f1206b5/dqc_reference/checkm_data
[2024-01-24 12:46:41,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:41,180] [INFO] Task started: CheckM
[2024-01-24 12:46:41,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862215.1_ASM1686221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862215.1_ASM1686221v1_genomic.fna/checkm_input GCF_016862215.1_ASM1686221v1_genomic.fna/checkm_result
[2024-01-24 12:48:58,169] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:58,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:58,202] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:58,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:58,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862215.1_ASM1686221v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:58,203] [INFO] Task started: Blastn
[2024-01-24 12:48:58,203] [INFO] Running command: blastn -query GCF_016862215.1_ASM1686221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ef39fbd-0012-41ad-8514-48fe4f1206b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862215.1_ASM1686221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:59,937] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:59,941] [INFO] Selected 10 target genomes.
[2024-01-24 12:48:59,941] [INFO] Target genome list was writen to GCF_016862215.1_ASM1686221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:59,949] [INFO] Task started: fastANI
[2024-01-24 12:48:59,949] [INFO] Running command: fastANI --query /var/lib/cwl/stge43fed57-87ee-45f6-885e-eafd5f6921ad/GCF_016862215.1_ASM1686221v1_genomic.fna.gz --refList GCF_016862215.1_ASM1686221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862215.1_ASM1686221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:24,665] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:24,677] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:24,677] [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_016862215.1	s__Actinoplanes humidus	100.0	3606	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018332715.1	s__Actinoplanes consettensis	94.7054	2988	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	82.5729	1911	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553785.1	s__Actinoplanes sp001553785	82.3841	1691	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464385.1	s__Actinoplanes sp016464385	82.2183	1704	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	82.0875	1657	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_014648355.1	s__Actinoplanes azureus	81.7714	1418	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	81.5218	1664	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	81.4996	1451	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000494755.1	s__Actinoplanes friuliensis	81.4313	1810	3616	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:24,679] [INFO] GTDB search result was written to GCF_016862215.1_ASM1686221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:24,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:24,683] [INFO] DFAST_QC result json was written to GCF_016862215.1_ASM1686221v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:24,684] [INFO] DFAST_QC completed!
[2024-01-24 12:49:24,684] [INFO] Total running time: 0h4m4s