[2024-01-24 10:57:11,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:11,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:11,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c5530b7-3728-4a47-ae75-9a6c3972a708/dqc_reference
[2024-01-24 10:57:12,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:12,613] [INFO] Task started: Prodigal
[2024-01-24 10:57:12,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e068712-f949-4dc0-862c-fc7adc5a4290/GCF_014145675.1_ASM1414567v1_genomic.fna.gz | prodigal -d GCF_014145675.1_ASM1414567v1_genomic.fna/cds.fna -a GCF_014145675.1_ASM1414567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:42,629] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:42,629] [INFO] Task started: HMMsearch
[2024-01-24 10:57:42,630] [INFO] Running command: hmmsearch --tblout GCF_014145675.1_ASM1414567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c5530b7-3728-4a47-ae75-9a6c3972a708/dqc_reference/reference_markers.hmm GCF_014145675.1_ASM1414567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:43,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:43,127] [INFO] Found 6/6 markers.
[2024-01-24 10:57:43,201] [INFO] Query marker FASTA was written to GCF_014145675.1_ASM1414567v1_genomic.fna/markers.fasta
[2024-01-24 10:57:43,201] [INFO] Task started: Blastn
[2024-01-24 10:57:43,201] [INFO] Running command: blastn -query GCF_014145675.1_ASM1414567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c5530b7-3728-4a47-ae75-9a6c3972a708/dqc_reference/reference_markers.fasta -out GCF_014145675.1_ASM1414567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:44,537] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:44,541] [INFO] Selected 13 target genomes.
[2024-01-24 10:57:44,541] [INFO] Target genome list was writen to GCF_014145675.1_ASM1414567v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:44,547] [INFO] Task started: fastANI
[2024-01-24 10:57:44,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e068712-f949-4dc0-862c-fc7adc5a4290/GCF_014145675.1_ASM1414567v1_genomic.fna.gz --refList GCF_014145675.1_ASM1414567v1_genomic.fna/target_genomes.txt --output GCF_014145675.1_ASM1414567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:14,527] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:14,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c5530b7-3728-4a47-ae75-9a6c3972a708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:14,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c5530b7-3728-4a47-ae75-9a6c3972a708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:14,544] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:14,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:14,544] [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 dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	100.0	3201	3203	95	conclusive
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	93.8385	2668	3203	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	93.6888	2511	3203	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	92.1772	2488	3203	95	below_threshold
Amycolatopsis benzoatilytica	strain=AK 16/65	GCA_000383915.1	346045	346045	type	True	86.6742	2034	3203	95	below_threshold
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	83.0678	1403	3203	95	below_threshold
Amycolatopsis panacis	strain=YIM PH21725	GCA_003600245.1	2340917	2340917	type	True	83.0037	1383	3203	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.4738	1665	3203	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.8014	1165	3203	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	79.4293	1162	3203	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.9305	983	3203	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	77.8236	822	3203	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	77.4411	776	3203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:14,545] [INFO] DFAST Taxonomy check result was written to GCF_014145675.1_ASM1414567v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:14,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:14,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:14,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c5530b7-3728-4a47-ae75-9a6c3972a708/dqc_reference/checkm_data
[2024-01-24 10:58:14,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:14,631] [INFO] Task started: CheckM
[2024-01-24 10:58:14,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145675.1_ASM1414567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145675.1_ASM1414567v1_genomic.fna/checkm_input GCF_014145675.1_ASM1414567v1_genomic.fna/checkm_result
[2024-01-24 10:59:45,668] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:45,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:45,695] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:45,696] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:45,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145675.1_ASM1414567v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:45,696] [INFO] Task started: Blastn
[2024-01-24 10:59:45,697] [INFO] Running command: blastn -query GCF_014145675.1_ASM1414567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c5530b7-3728-4a47-ae75-9a6c3972a708/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145675.1_ASM1414567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:47,680] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:47,683] [INFO] Selected 12 target genomes.
[2024-01-24 10:59:47,683] [INFO] Target genome list was writen to GCF_014145675.1_ASM1414567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:47,692] [INFO] Task started: fastANI
[2024-01-24 10:59:47,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e068712-f949-4dc0-862c-fc7adc5a4290/GCF_014145675.1_ASM1414567v1_genomic.fna.gz --refList GCF_014145675.1_ASM1414567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145675.1_ASM1414567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:16,077] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:16,094] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:16,094] [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_014145675.1	s__Amycolatopsis sp014145675	100.0	3201	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004522235.1	s__Amycolatopsis nivea	93.8378	2667	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_900115345.1	s__Amycolatopsis rubida	93.6796	2512	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.28	99.27	0.88	0.87	4	-
GCF_002796545.1	s__Amycolatopsis sp002796545	92.7284	2494	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014174495.1	s__Amycolatopsis echigonensis	92.2377	2318	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	98.67	98.67	0.88	0.88	2	-
GCF_003385235.1	s__Amycolatopsis circi	92.1775	2486	3203	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	92.1661	2350	3203	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	86.6433	2039	3203	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	85.2537	1874	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564045.1	s__Amycolatopsis sulphurea	83.0906	1399	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	95.19	95.19	0.83	0.83	2	-
GCF_016889705.1	s__Amycolatopsis sp016889705	82.4097	1608	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647915.1	s__Pilimelia terevasa	76.01	456	3203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:16,096] [INFO] GTDB search result was written to GCF_014145675.1_ASM1414567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:16,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:16,100] [INFO] DFAST_QC result json was written to GCF_014145675.1_ASM1414567v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:16,100] [INFO] DFAST_QC completed!
[2024-01-24 11:00:16,100] [INFO] Total running time: 0h3m5s