[2024-01-24 15:26:39,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,070] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg645dbeb8-f976-4539-ad82-7ab383f3ecd7/dqc_reference
[2024-01-24 15:26:40,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,468] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg0845a846-e024-44dc-9713-f30b85828091/GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/cds.fna -a GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:50,064] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:50,065] [INFO] Task started: HMMsearch
[2024-01-24 15:26:50,065] [INFO] Running command: hmmsearch --tblout GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg645dbeb8-f976-4539-ad82-7ab383f3ecd7/dqc_reference/reference_markers.hmm GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:50,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:50,378] [INFO] Found 6/6 markers.
[2024-01-24 15:26:50,412] [INFO] Query marker FASTA was written to GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:26:50,413] [INFO] Task started: Blastn
[2024-01-24 15:26:50,413] [INFO] Running command: blastn -query GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg645dbeb8-f976-4539-ad82-7ab383f3ecd7/dqc_reference/reference_markers.fasta -out GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:51,091] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:51,095] [INFO] Selected 16 target genomes.
[2024-01-24 15:26:51,095] [INFO] Target genome list was writen to GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:26:51,108] [INFO] Task started: fastANI
[2024-01-24 15:26:51,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg0845a846-e024-44dc-9713-f30b85828091/GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna.gz --refList GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:03,912] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:03,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg645dbeb8-f976-4539-ad82-7ab383f3ecd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:03,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg645dbeb8-f976-4539-ad82-7ab383f3ecd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:03,919] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:03,920] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:03,920] [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
Anaerotignum lactatifermentans	strain=DSM 14214	GCA_900142265.1	160404	160404	suspected-type	True	100.0	1090	1101	95	conclusive
Anaerotignum faecicola	strain=KCTC 15736	GCA_003865035.1	2358141	2358141	type	True	80.1274	217	1101	95	below_threshold
Anaerotignum propionicum	strain=X2	GCA_001561955.1	28446	28446	type	True	77.7229	105	1101	95	below_threshold
Anaerotignum propionicum	strain=DSM 1682	GCA_900129165.1	28446	28446	type	True	77.6096	106	1101	95	below_threshold
Anaerotignum neopropionicum	strain=DSM-3847	GCA_001571775.1	36847	36847	type	True	77.3278	109	1101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:03,923] [INFO] DFAST Taxonomy check result was written to GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:27:03,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:03,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:03,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg645dbeb8-f976-4539-ad82-7ab383f3ecd7/dqc_reference/checkm_data
[2024-01-24 15:27:03,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:03,964] [INFO] Task started: CheckM
[2024-01-24 15:27:03,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/checkm_input GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:27:37,531] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:37,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,552] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:37,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:37,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:27:37,553] [INFO] Task started: Blastn
[2024-01-24 15:27:37,553] [INFO] Running command: blastn -query GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg645dbeb8-f976-4539-ad82-7ab383f3ecd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:38,570] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:38,576] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:38,576] [INFO] Target genome list was writen to GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:38,587] [INFO] Task started: fastANI
[2024-01-24 15:27:38,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg0845a846-e024-44dc-9713-f30b85828091/GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna.gz --refList GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:46,006] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:46,014] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:46,014] [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_900142265.1	s__Anaerotignum lactatifermentans	100.0	1090	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	97.69	96.94	0.89	0.80	7	conclusive
GCA_905212195.1	s__Anaerotignum sp905212195	94.7391	602	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001304995.1	s__Anaerotignum sp001304995	92.1502	735	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	98.57	97.74	0.93	0.89	6	-
GCF_016902535.1	s__Anaerotignum lactatifermentans_A	81.5368	390	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017483025.1	s__Anaerotignum sp017483025	79.8267	233	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557645.1	s__Anaerotignum sp004557645	79.8174	245	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115165.1	s__Anaerotignum merdipullorum	79.4576	252	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	99.63	99.27	0.89	0.86	3	-
GCA_017560955.1	s__Anaerotignum sp017560955	79.2026	136	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214825.1	s__Anaerotignum sp905214825	78.4458	148	1101	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:46,016] [INFO] GTDB search result was written to GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:46,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:46,019] [INFO] DFAST_QC result json was written to GCF_900142265.1_IMG-taxon_2585428190_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:27:46,019] [INFO] DFAST_QC completed!
[2024-01-24 15:27:46,019] [INFO] Total running time: 0h1m7s