[2024-01-24 11:51:50,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg15e80b4e-2c0c-4186-8d6b-8f19f63de54d/dqc_reference
[2024-01-24 11:51:51,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,638] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b88fdc2-6532-4574-9622-726b8951098e/GCF_002156025.1_ASM215602v1_genomic.fna.gz | prodigal -d GCF_002156025.1_ASM215602v1_genomic.fna/cds.fna -a GCF_002156025.1_ASM215602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:17,516] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:17,517] [INFO] Task started: HMMsearch
[2024-01-24 11:52:17,517] [INFO] Running command: hmmsearch --tblout GCF_002156025.1_ASM215602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15e80b4e-2c0c-4186-8d6b-8f19f63de54d/dqc_reference/reference_markers.hmm GCF_002156025.1_ASM215602v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:17,938] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:17,940] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7b88fdc2-6532-4574-9622-726b8951098e/GCF_002156025.1_ASM215602v1_genomic.fna.gz]
[2024-01-24 11:52:18,027] [INFO] Query marker FASTA was written to GCF_002156025.1_ASM215602v1_genomic.fna/markers.fasta
[2024-01-24 11:52:18,027] [INFO] Task started: Blastn
[2024-01-24 11:52:18,028] [INFO] Running command: blastn -query GCF_002156025.1_ASM215602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15e80b4e-2c0c-4186-8d6b-8f19f63de54d/dqc_reference/reference_markers.fasta -out GCF_002156025.1_ASM215602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:19,409] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:19,413] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:19,414] [INFO] Target genome list was writen to GCF_002156025.1_ASM215602v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:19,425] [INFO] Task started: fastANI
[2024-01-24 11:52:19,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b88fdc2-6532-4574-9622-726b8951098e/GCF_002156025.1_ASM215602v1_genomic.fna.gz --refList GCF_002156025.1_ASM215602v1_genomic.fna/target_genomes.txt --output GCF_002156025.1_ASM215602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:52,872] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:52,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15e80b4e-2c0c-4186-8d6b-8f19f63de54d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:52,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15e80b4e-2c0c-4186-8d6b-8f19f63de54d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:52,887] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:52,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:52,888] [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 pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	100.0	3080	3110	95	conclusive
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	99.9903	3095	3110	95	conclusive
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	91.0043	2473	3110	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	89.4128	2355	3110	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	89.349	2389	3110	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	89.3121	2127	3110	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	88.9097	1892	3110	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	88.8649	2265	3110	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	88.6339	1957	3110	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	88.6317	2253	3110	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.1732	1224	3110	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0467	1057	3110	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	78.74	771	3110	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.6861	987	3110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:52,891] [INFO] DFAST Taxonomy check result was written to GCF_002156025.1_ASM215602v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:52,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:52,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:52,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15e80b4e-2c0c-4186-8d6b-8f19f63de54d/dqc_reference/checkm_data
[2024-01-24 11:52:52,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:52,983] [INFO] Task started: CheckM
[2024-01-24 11:52:52,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002156025.1_ASM215602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002156025.1_ASM215602v1_genomic.fna/checkm_input GCF_002156025.1_ASM215602v1_genomic.fna/checkm_result
[2024-01-24 11:54:46,852] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:46,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:46,887] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:46,888] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:46,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002156025.1_ASM215602v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:46,889] [INFO] Task started: Blastn
[2024-01-24 11:54:46,889] [INFO] Running command: blastn -query GCF_002156025.1_ASM215602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15e80b4e-2c0c-4186-8d6b-8f19f63de54d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002156025.1_ASM215602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:49,179] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:49,185] [INFO] Selected 14 target genomes.
[2024-01-24 11:54:49,185] [INFO] Target genome list was writen to GCF_002156025.1_ASM215602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:49,207] [INFO] Task started: fastANI
[2024-01-24 11:54:49,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b88fdc2-6532-4574-9622-726b8951098e/GCF_002156025.1_ASM215602v1_genomic.fna.gz --refList GCF_002156025.1_ASM215602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002156025.1_ASM215602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:55:27,534] [INFO] Task succeeded: fastANI
[2024-01-24 11:55:27,553] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:55:27,554] [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_900107925.1	s__Amycolatopsis pretoriensis	99.9903	3095	3110	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_902497555.1	s__Amycolatopsis sp902497555	90.9738	2478	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937945.1	s__Amycolatopsis eburnea	89.3942	2358	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873755.1	s__Amycolatopsis lexingtonensis	89.3303	2392	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	88.8839	2261	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014654205.1	s__Amycolatopsis bullii	88.682	2179	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904295.1	s__Amycolatopsis sp002904295	88.6411	2251	3110	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	88.639	2252	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_002155975.1	s__Amycolatopsis kentuckyensis	88.6164	1960	3110	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	88.6128	2278	3110	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	88.5878	2205	3110	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	88.5409	2166	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234595.1	s__Amycolatopsis vastitatis	88.4134	2137	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384295.1	s__Amycolatopsis balhimycina	88.2473	2159	3110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:55:27,556] [INFO] GTDB search result was written to GCF_002156025.1_ASM215602v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:55:27,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:55:27,560] [INFO] DFAST_QC result json was written to GCF_002156025.1_ASM215602v1_genomic.fna/dqc_result.json
[2024-01-24 11:55:27,560] [INFO] DFAST_QC completed!
[2024-01-24 11:55:27,560] [INFO] Total running time: 0h3m37s