[2024-01-24 14:05:47,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:47,207] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:47,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e20681c-6b33-4c9b-b31b-64548b8719ad/dqc_reference
[2024-01-24 14:05:48,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:48,534] [INFO] Task started: Prodigal
[2024-01-24 14:05:48,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg72c03481-abfb-409e-b0ef-10c62ec67b68/GCF_003600245.1_ASM360024v1_genomic.fna.gz | prodigal -d GCF_003600245.1_ASM360024v1_genomic.fna/cds.fna -a GCF_003600245.1_ASM360024v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:09,842] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:09,843] [INFO] Task started: HMMsearch
[2024-01-24 14:06:09,843] [INFO] Running command: hmmsearch --tblout GCF_003600245.1_ASM360024v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e20681c-6b33-4c9b-b31b-64548b8719ad/dqc_reference/reference_markers.hmm GCF_003600245.1_ASM360024v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:10,174] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:10,176] [INFO] Found 6/6 markers.
[2024-01-24 14:06:10,235] [INFO] Query marker FASTA was written to GCF_003600245.1_ASM360024v1_genomic.fna/markers.fasta
[2024-01-24 14:06:10,236] [INFO] Task started: Blastn
[2024-01-24 14:06:10,236] [INFO] Running command: blastn -query GCF_003600245.1_ASM360024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e20681c-6b33-4c9b-b31b-64548b8719ad/dqc_reference/reference_markers.fasta -out GCF_003600245.1_ASM360024v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:11,566] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:11,570] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:11,571] [INFO] Target genome list was writen to GCF_003600245.1_ASM360024v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:11,580] [INFO] Task started: fastANI
[2024-01-24 14:06:11,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg72c03481-abfb-409e-b0ef-10c62ec67b68/GCF_003600245.1_ASM360024v1_genomic.fna.gz --refList GCF_003600245.1_ASM360024v1_genomic.fna/target_genomes.txt --output GCF_003600245.1_ASM360024v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:45,193] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:45,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e20681c-6b33-4c9b-b31b-64548b8719ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:45,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e20681c-6b33-4c9b-b31b-64548b8719ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:45,209] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:45,210] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:06:45,210] [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 panacis	strain=YIM PH21725	GCA_003600245.1	2340917	2340917	type	True	100.0	2243	2252	95	inconclusive
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	95.1974	1875	2252	95	inconclusive
Amycolatopsis jiangsuensis	strain=DSM 45859	GCA_014204865.1	1181879	1181879	type	True	85.9324	1489	2252	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	83.1594	1364	2252	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	83.1016	1307	2252	95	below_threshold
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	83.0824	1367	2252	95	below_threshold
Amycolatopsis benzoatilytica	strain=AK 16/65	GCA_000383915.1	346045	346045	type	True	83.0181	1367	2252	95	below_threshold
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	82.9749	1392	2252	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	82.9677	1331	2252	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	82.7862	1373	2252	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.0783	1215	2252	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	80.4083	1019	2252	95	below_threshold
Amycolatopsis regifaucium	strain=DSM 45072	GCA_900113515.1	546365	546365	type	True	80.406	1010	2252	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001558125.2	546365	546365	type	True	80.3668	1018	2252	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.0242	916	2252	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	79.881	920	2252	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.1296	775	2252	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	76.6792	378	2252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:45,212] [INFO] DFAST Taxonomy check result was written to GCF_003600245.1_ASM360024v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:45,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:45,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:45,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e20681c-6b33-4c9b-b31b-64548b8719ad/dqc_reference/checkm_data
[2024-01-24 14:06:45,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:45,285] [INFO] Task started: CheckM
[2024-01-24 14:06:45,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003600245.1_ASM360024v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003600245.1_ASM360024v1_genomic.fna/checkm_input GCF_003600245.1_ASM360024v1_genomic.fna/checkm_result
[2024-01-24 14:07:52,990] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:52,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:53,008] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:53,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:53,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003600245.1_ASM360024v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:53,009] [INFO] Task started: Blastn
[2024-01-24 14:07:53,010] [INFO] Running command: blastn -query GCF_003600245.1_ASM360024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e20681c-6b33-4c9b-b31b-64548b8719ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_003600245.1_ASM360024v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:54,930] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:54,934] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:54,934] [INFO] Target genome list was writen to GCF_003600245.1_ASM360024v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:54,944] [INFO] Task started: fastANI
[2024-01-24 14:07:54,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg72c03481-abfb-409e-b0ef-10c62ec67b68/GCF_003600245.1_ASM360024v1_genomic.fna.gz --refList GCF_003600245.1_ASM360024v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003600245.1_ASM360024v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:23,982] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:23,994] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:23,995] [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_002564045.1	s__Amycolatopsis sulphurea	95.1887	1876	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	95.19	95.19	0.83	0.83	2	conclusive
GCF_014204865.1	s__Amycolatopsis jiangsuensis	85.8831	1496	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411975.1	s__Amycolatopsis orientalis_D	83.2967	1347	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796545.1	s__Amycolatopsis sp002796545	83.1769	1370	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900115345.1	s__Amycolatopsis rubida	83.1532	1365	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.28	99.27	0.88	0.87	4	-
GCF_003385235.1	s__Amycolatopsis circi	83.1005	1306	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145675.1	s__Amycolatopsis sp014145675	83.0913	1365	2252	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	83.0575	1361	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174495.1	s__Amycolatopsis echigonensis	83.0575	1334	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	98.67	98.67	0.88	0.88	2	-
GCF_000717335.1	s__Amycolatopsis jejuensis	82.9959	1326	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110575.1	s__Amycolatopsis saalfeldensis	82.7395	1383	2252	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	81.0789	1183	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613935.1	s__Amycolatopsis regifaucium	80.4031	1021	2252	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:23,996] [INFO] GTDB search result was written to GCF_003600245.1_ASM360024v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:23,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:24,001] [INFO] DFAST_QC result json was written to GCF_003600245.1_ASM360024v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:24,001] [INFO] DFAST_QC completed!
[2024-01-24 14:08:24,001] [INFO] Total running time: 0h2m37s