[2024-01-24 12:48:20,278] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:20,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:20,280] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1fcd144-61f0-4cb0-a403-31fcf102c3a4/dqc_reference
[2024-01-24 12:48:21,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:21,475] [INFO] Task started: Prodigal
[2024-01-24 12:48:21,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg237d1d38-0f0f-49dd-b54f-5b3c1d4a6785/GCF_004364975.1_ASM436497v1_genomic.fna.gz | prodigal -d GCF_004364975.1_ASM436497v1_genomic.fna/cds.fna -a GCF_004364975.1_ASM436497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:36,123] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:36,124] [INFO] Task started: HMMsearch
[2024-01-24 12:48:36,124] [INFO] Running command: hmmsearch --tblout GCF_004364975.1_ASM436497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1fcd144-61f0-4cb0-a403-31fcf102c3a4/dqc_reference/reference_markers.hmm GCF_004364975.1_ASM436497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:36,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:36,406] [INFO] Found 6/6 markers.
[2024-01-24 12:48:36,443] [INFO] Query marker FASTA was written to GCF_004364975.1_ASM436497v1_genomic.fna/markers.fasta
[2024-01-24 12:48:36,443] [INFO] Task started: Blastn
[2024-01-24 12:48:36,444] [INFO] Running command: blastn -query GCF_004364975.1_ASM436497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1fcd144-61f0-4cb0-a403-31fcf102c3a4/dqc_reference/reference_markers.fasta -out GCF_004364975.1_ASM436497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:37,130] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:37,134] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:37,134] [INFO] Target genome list was writen to GCF_004364975.1_ASM436497v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:37,148] [INFO] Task started: fastANI
[2024-01-24 12:48:37,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg237d1d38-0f0f-49dd-b54f-5b3c1d4a6785/GCF_004364975.1_ASM436497v1_genomic.fna.gz --refList GCF_004364975.1_ASM436497v1_genomic.fna/target_genomes.txt --output GCF_004364975.1_ASM436497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:47,602] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:47,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1fcd144-61f0-4cb0-a403-31fcf102c3a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:47,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1fcd144-61f0-4cb0-a403-31fcf102c3a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:47,620] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:47,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:47,621] [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
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	100.0	1180	1180	95	conclusive
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	83.1541	800	1180	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	79.9391	592	1180	95	below_threshold
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	79.9141	588	1180	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	79.0636	516	1180	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	79.0161	530	1180	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	78.8747	527	1180	95	below_threshold
Gelidibacter maritimus	strain=F6074	GCA_014062315.1	2761487	2761487	type	True	78.5705	518	1180	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.7481	155	1180	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	77.704	178	1180	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.1014	142	1180	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.091	153	1180	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.9022	126	1180	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.863	122	1180	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	76.6403	92	1180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:47,623] [INFO] DFAST Taxonomy check result was written to GCF_004364975.1_ASM436497v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:47,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:47,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:47,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1fcd144-61f0-4cb0-a403-31fcf102c3a4/dqc_reference/checkm_data
[2024-01-24 12:48:47,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:47,664] [INFO] Task started: CheckM
[2024-01-24 12:48:47,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004364975.1_ASM436497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004364975.1_ASM436497v1_genomic.fna/checkm_input GCF_004364975.1_ASM436497v1_genomic.fna/checkm_result
[2024-01-24 12:49:32,264] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:32,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:32,287] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:32,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:32,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004364975.1_ASM436497v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:32,288] [INFO] Task started: Blastn
[2024-01-24 12:49:32,288] [INFO] Running command: blastn -query GCF_004364975.1_ASM436497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1fcd144-61f0-4cb0-a403-31fcf102c3a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004364975.1_ASM436497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:33,259] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:33,263] [INFO] Selected 9 target genomes.
[2024-01-24 12:49:33,263] [INFO] Target genome list was writen to GCF_004364975.1_ASM436497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:33,275] [INFO] Task started: fastANI
[2024-01-24 12:49:33,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg237d1d38-0f0f-49dd-b54f-5b3c1d4a6785/GCF_004364975.1_ASM436497v1_genomic.fna.gz --refList GCF_004364975.1_ASM436497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004364975.1_ASM436497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:41,607] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:41,615] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:41,615] [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_004364975.1	s__Gelidibacter sediminis	100.0	1180	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007997285.1	s__Gelidibacter salicanalis	83.1432	801	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016469035.1	s__Gelidibacter salicanalis_A	81.913	785	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678675.1	s__Gelidibacter algens	79.9183	588	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCF_004115975.1	s__Gelidibacter gilvus	79.0686	516	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423005.1	s__Gelidibacter mesophilus	79.0078	531	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017581925.1	s__Gelidibacter sp017581925	78.8745	527	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014062315.1	s__Gelidibacter sp014062315	78.5675	519	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265225.1	s__Tamlana_C fucoidanivorans	77.2323	121	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:41,617] [INFO] GTDB search result was written to GCF_004364975.1_ASM436497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:41,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:41,620] [INFO] DFAST_QC result json was written to GCF_004364975.1_ASM436497v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:41,621] [INFO] DFAST_QC completed!
[2024-01-24 12:49:41,621] [INFO] Total running time: 0h1m21s