[2024-01-24 12:23:50,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg8af02f7d-d9f6-4eea-a65b-7eaba94893bb/dqc_reference
[2024-01-24 12:23:52,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,203] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,203] [INFO] Running command: gunzip -c /var/lib/cwl/stg21cfe339-8883-45c9-950e-943480e9c952/GCF_014873755.1_ASM1487375v1_genomic.fna.gz | prodigal -d GCF_014873755.1_ASM1487375v1_genomic.fna/cds.fna -a GCF_014873755.1_ASM1487375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:31,358] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:31,358] [INFO] Task started: HMMsearch
[2024-01-24 12:24:31,359] [INFO] Running command: hmmsearch --tblout GCF_014873755.1_ASM1487375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8af02f7d-d9f6-4eea-a65b-7eaba94893bb/dqc_reference/reference_markers.hmm GCF_014873755.1_ASM1487375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:31,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:31,773] [INFO] Found 6/6 markers.
[2024-01-24 12:24:31,859] [INFO] Query marker FASTA was written to GCF_014873755.1_ASM1487375v1_genomic.fna/markers.fasta
[2024-01-24 12:24:31,860] [INFO] Task started: Blastn
[2024-01-24 12:24:31,860] [INFO] Running command: blastn -query GCF_014873755.1_ASM1487375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8af02f7d-d9f6-4eea-a65b-7eaba94893bb/dqc_reference/reference_markers.fasta -out GCF_014873755.1_ASM1487375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:33,258] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:33,263] [INFO] Selected 16 target genomes.
[2024-01-24 12:24:33,263] [INFO] Target genome list was writen to GCF_014873755.1_ASM1487375v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:33,269] [INFO] Task started: fastANI
[2024-01-24 12:24:33,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cfe339-8883-45c9-950e-943480e9c952/GCF_014873755.1_ASM1487375v1_genomic.fna.gz --refList GCF_014873755.1_ASM1487375v1_genomic.fna/target_genomes.txt --output GCF_014873755.1_ASM1487375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:25:18,913] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:18,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8af02f7d-d9f6-4eea-a65b-7eaba94893bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:25:18,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8af02f7d-d9f6-4eea-a65b-7eaba94893bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:25:18,926] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:25:18,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:25:18,926] [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
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	100.0	3578	3579	95	conclusive
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	99.8187	3023	3579	95	conclusive
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	94.3672	2922	3579	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	89.4884	2610	3579	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	89.4048	2377	3579	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	89.3198	2669	3579	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	89.2104	2114	3579	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	89.1423	2570	3579	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	89.0786	2214	3579	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	89.0211	2485	3579	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	88.7384	2532	3579	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	80.9535	1492	3579	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.2648	1332	3579	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.2899	1170	3579	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7715	1126	3579	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.1022	1024	3579	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:25:18,930] [INFO] DFAST Taxonomy check result was written to GCF_014873755.1_ASM1487375v1_genomic.fna/tc_result.tsv
[2024-01-24 12:25:18,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:25:18,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:25:18,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8af02f7d-d9f6-4eea-a65b-7eaba94893bb/dqc_reference/checkm_data
[2024-01-24 12:25:18,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:25:19,026] [INFO] Task started: CheckM
[2024-01-24 12:25:19,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873755.1_ASM1487375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873755.1_ASM1487375v1_genomic.fna/checkm_input GCF_014873755.1_ASM1487375v1_genomic.fna/checkm_result
[2024-01-24 12:27:50,333] [INFO] Task succeeded: CheckM
[2024-01-24 12:27:50,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:27:50,367] [INFO] ===== Completeness check finished =====
[2024-01-24 12:27:50,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:27:50,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873755.1_ASM1487375v1_genomic.fna/markers.fasta)
[2024-01-24 12:27:50,368] [INFO] Task started: Blastn
[2024-01-24 12:27:50,368] [INFO] Running command: blastn -query GCF_014873755.1_ASM1487375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8af02f7d-d9f6-4eea-a65b-7eaba94893bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873755.1_ASM1487375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:52,443] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:52,447] [INFO] Selected 13 target genomes.
[2024-01-24 12:27:52,447] [INFO] Target genome list was writen to GCF_014873755.1_ASM1487375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:27:52,537] [INFO] Task started: fastANI
[2024-01-24 12:27:52,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cfe339-8883-45c9-950e-943480e9c952/GCF_014873755.1_ASM1487375v1_genomic.fna.gz --refList GCF_014873755.1_ASM1487375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873755.1_ASM1487375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:34,099] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:34,116] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:34,116] [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_014873755.1	s__Amycolatopsis lexingtonensis	100.0	3578	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003937945.1	s__Amycolatopsis eburnea	94.3807	2920	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107925.1	s__Amycolatopsis pretoriensis	89.4834	2611	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_902497555.1	s__Amycolatopsis sp902497555	89.321	2667	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	89.1647	2565	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002155975.1	s__Amycolatopsis kentuckyensis	89.117	2208	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220945.1	s__Amycolatopsis mediterranei	89.0161	2485	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_014654205.1	s__Amycolatopsis bullii	88.9278	2421	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904335.1	s__Amycolatopsis sp002904335	88.8986	2480	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308975.1	s__Amycolatopsis sp017308975	88.7861	2463	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	88.7553	2530	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383915.1	s__Amycolatopsis benzoatilytica	81.6453	1657	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717335.1	s__Amycolatopsis jejuensis	80.9466	1492	3579	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:28:34,119] [INFO] GTDB search result was written to GCF_014873755.1_ASM1487375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:34,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:34,126] [INFO] DFAST_QC result json was written to GCF_014873755.1_ASM1487375v1_genomic.fna/dqc_result.json
[2024-01-24 12:28:34,126] [INFO] DFAST_QC completed!
[2024-01-24 12:28:34,126] [INFO] Total running time: 0h4m43s