[2024-01-24 13:57:42,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbf61f5c-f4a3-4254-9ee6-60f35d38da48/dqc_reference
[2024-01-24 13:57:44,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,342] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c66bfad-ec43-44ec-a159-701f843aeba3/GCF_019396355.1_ASM1939635v1_genomic.fna.gz | prodigal -d GCF_019396355.1_ASM1939635v1_genomic.fna/cds.fna -a GCF_019396355.1_ASM1939635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:09,539] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:09,540] [INFO] Task started: HMMsearch
[2024-01-24 13:58:09,540] [INFO] Running command: hmmsearch --tblout GCF_019396355.1_ASM1939635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbf61f5c-f4a3-4254-9ee6-60f35d38da48/dqc_reference/reference_markers.hmm GCF_019396355.1_ASM1939635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:09,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:09,991] [INFO] Found 6/6 markers.
[2024-01-24 13:58:10,069] [INFO] Query marker FASTA was written to GCF_019396355.1_ASM1939635v1_genomic.fna/markers.fasta
[2024-01-24 13:58:10,070] [INFO] Task started: Blastn
[2024-01-24 13:58:10,070] [INFO] Running command: blastn -query GCF_019396355.1_ASM1939635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf61f5c-f4a3-4254-9ee6-60f35d38da48/dqc_reference/reference_markers.fasta -out GCF_019396355.1_ASM1939635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:11,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:11,576] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:11,576] [INFO] Target genome list was writen to GCF_019396355.1_ASM1939635v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:11,580] [INFO] Task started: fastANI
[2024-01-24 13:58:11,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c66bfad-ec43-44ec-a159-701f843aeba3/GCF_019396355.1_ASM1939635v1_genomic.fna.gz --refList GCF_019396355.1_ASM1939635v1_genomic.fna/target_genomes.txt --output GCF_019396355.1_ASM1939635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:31,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:31,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbf61f5c-f4a3-4254-9ee6-60f35d38da48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:31,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbf61f5c-f4a3-4254-9ee6-60f35d38da48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:31,046] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:31,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:31,047] [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
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	100.0	2526	2553	95	conclusive
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	82.5139	1480	2553	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	81.9432	1174	2553	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	81.7327	1347	2553	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	81.7235	1380	2553	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	81.2732	1223	2553	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	80.8591	1204	2553	95	below_threshold
Pseudonocardia asaccharolytica	strain=DSM 44247	GCA_000423625.1	54010	54010	type	True	79.9293	859	2553	95	below_threshold
Pseudonocardia asaccharolytica	strain=NBRC 16224	GCA_007989065.1	54010	54010	type	True	79.916	863	2553	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	79.4545	964	2553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:31,048] [INFO] DFAST Taxonomy check result was written to GCF_019396355.1_ASM1939635v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:31,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:31,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:31,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbf61f5c-f4a3-4254-9ee6-60f35d38da48/dqc_reference/checkm_data
[2024-01-24 13:58:31,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:31,127] [INFO] Task started: CheckM
[2024-01-24 13:58:31,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019396355.1_ASM1939635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019396355.1_ASM1939635v1_genomic.fna/checkm_input GCF_019396355.1_ASM1939635v1_genomic.fna/checkm_result
[2024-01-24 13:59:58,476] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:58,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:58,512] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:58,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:58,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019396355.1_ASM1939635v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:58,514] [INFO] Task started: Blastn
[2024-01-24 13:59:58,514] [INFO] Running command: blastn -query GCF_019396355.1_ASM1939635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf61f5c-f4a3-4254-9ee6-60f35d38da48/dqc_reference/reference_markers_gtdb.fasta -out GCF_019396355.1_ASM1939635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:00,688] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:00,696] [INFO] Selected 13 target genomes.
[2024-01-24 14:00:00,696] [INFO] Target genome list was writen to GCF_019396355.1_ASM1939635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:00,721] [INFO] Task started: fastANI
[2024-01-24 14:00:00,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c66bfad-ec43-44ec-a159-701f843aeba3/GCF_019396355.1_ASM1939635v1_genomic.fna.gz --refList GCF_019396355.1_ASM1939635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019396355.1_ASM1939635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:26,682] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:26,694] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:00:26,694] [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_006716445.1	s__Pseudonocardia kunmingensis	82.5406	1475	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262885.1	s__Pseudonocardia sp002262885	82.2424	1468	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911925.1	s__Pseudonocardia xinjiangensis	81.9293	1176	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	81.7606	1343	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	81.7481	1376	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942185.1	s__Pseudonocardia sp001942185	81.4652	1338	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942415.1	s__Pseudonocardia sp001942415	81.2102	1176	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263585.1	s__Pseudonocardia sp019263585	80.9133	1194	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
GCF_012911875.1	s__Pseudonocardia bannensis	80.4945	955	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531445.1	s__Pseudonocardia sp018531445	80.4691	1175	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423625.1	s__Pseudonocardia asaccharolytica	79.923	861	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002583555.1	s__Pseudonocardia sp002583555	79.5086	928	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989085.1	s__Pseudonocardia sulfidoxydans	79.5073	954	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:26,696] [INFO] GTDB search result was written to GCF_019396355.1_ASM1939635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:26,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:26,700] [INFO] DFAST_QC result json was written to GCF_019396355.1_ASM1939635v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:26,700] [INFO] DFAST_QC completed!
[2024-01-24 14:00:26,700] [INFO] Total running time: 0h2m44s