[2024-01-24 12:16:08,767] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ba552c3-69c0-4d1e-a202-8f6374287c1c/dqc_reference
[2024-01-24 12:16:10,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:10,146] [INFO] Task started: Prodigal
[2024-01-24 12:16:10,146] [INFO] Running command: gunzip -c /var/lib/cwl/stgb26e8d9e-cf67-4a2b-8afb-90290635dea4/GCF_017581925.1_ASM1758192v1_genomic.fna.gz | prodigal -d GCF_017581925.1_ASM1758192v1_genomic.fna/cds.fna -a GCF_017581925.1_ASM1758192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:29,675] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:29,676] [INFO] Task started: HMMsearch
[2024-01-24 12:16:29,676] [INFO] Running command: hmmsearch --tblout GCF_017581925.1_ASM1758192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ba552c3-69c0-4d1e-a202-8f6374287c1c/dqc_reference/reference_markers.hmm GCF_017581925.1_ASM1758192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:29,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:29,967] [INFO] Found 6/6 markers.
[2024-01-24 12:16:30,009] [INFO] Query marker FASTA was written to GCF_017581925.1_ASM1758192v1_genomic.fna/markers.fasta
[2024-01-24 12:16:30,009] [INFO] Task started: Blastn
[2024-01-24 12:16:30,009] [INFO] Running command: blastn -query GCF_017581925.1_ASM1758192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba552c3-69c0-4d1e-a202-8f6374287c1c/dqc_reference/reference_markers.fasta -out GCF_017581925.1_ASM1758192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:30,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:30,696] [INFO] Selected 12 target genomes.
[2024-01-24 12:16:30,697] [INFO] Target genome list was writen to GCF_017581925.1_ASM1758192v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:30,699] [INFO] Task started: fastANI
[2024-01-24 12:16:30,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26e8d9e-cf67-4a2b-8afb-90290635dea4/GCF_017581925.1_ASM1758192v1_genomic.fna.gz --refList GCF_017581925.1_ASM1758192v1_genomic.fna/target_genomes.txt --output GCF_017581925.1_ASM1758192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:40,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:40,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ba552c3-69c0-4d1e-a202-8f6374287c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:40,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ba552c3-69c0-4d1e-a202-8f6374287c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:40,535] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:40,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:40,536] [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 pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	100.0	1460	1461	95	conclusive
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	86.498	1117	1461	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	85.7639	1091	1461	95	below_threshold
Gelidibacter maritimus	strain=F6074	GCA_014062315.1	2761487	2761487	type	True	85.2989	1164	1461	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	81.1568	857	1461	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	79.3222	660	1461	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	78.7662	543	1461	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.9004	133	1461	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7654	141	1461	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.6171	106	1461	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.4862	104	1461	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.2875	130	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:40,537] [INFO] DFAST Taxonomy check result was written to GCF_017581925.1_ASM1758192v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:40,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:40,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:40,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ba552c3-69c0-4d1e-a202-8f6374287c1c/dqc_reference/checkm_data
[2024-01-24 12:16:40,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:40,584] [INFO] Task started: CheckM
[2024-01-24 12:16:40,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017581925.1_ASM1758192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017581925.1_ASM1758192v1_genomic.fna/checkm_input GCF_017581925.1_ASM1758192v1_genomic.fna/checkm_result
[2024-01-24 12:17:37,863] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:37,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:37,886] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:37,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:37,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017581925.1_ASM1758192v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:37,887] [INFO] Task started: Blastn
[2024-01-24 12:17:37,887] [INFO] Running command: blastn -query GCF_017581925.1_ASM1758192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba552c3-69c0-4d1e-a202-8f6374287c1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017581925.1_ASM1758192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:38,796] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:38,801] [INFO] Selected 8 target genomes.
[2024-01-24 12:17:38,801] [INFO] Target genome list was writen to GCF_017581925.1_ASM1758192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:38,809] [INFO] Task started: fastANI
[2024-01-24 12:17:38,810] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26e8d9e-cf67-4a2b-8afb-90290635dea4/GCF_017581925.1_ASM1758192v1_genomic.fna.gz --refList GCF_017581925.1_ASM1758192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017581925.1_ASM1758192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:47,963] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:47,979] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:47,979] [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_017581925.1	s__Gelidibacter sp017581925	100.0	1460	1461	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_010725055.1	s__Gelidibacter japonicus	86.4607	1119	1461	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004115975.1	s__Gelidibacter gilvus	85.7639	1091	1461	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	85.31	1163	1461	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	81.1513	858	1461	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	79.3491	659	1461	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	79.2992	643	1461	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCF_004364975.1	s__Gelidibacter sediminis	78.7735	542	1461	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:47,982] [INFO] GTDB search result was written to GCF_017581925.1_ASM1758192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:47,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:47,988] [INFO] DFAST_QC result json was written to GCF_017581925.1_ASM1758192v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:47,988] [INFO] DFAST_QC completed!
[2024-01-24 12:17:47,988] [INFO] Total running time: 0h1m39s