[2024-01-24 14:03:04,776] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:04,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:04,781] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6d33683-d76a-4074-b53e-16822c07c7d4/dqc_reference
[2024-01-24 14:03:06,031] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:06,032] [INFO] Task started: Prodigal
[2024-01-24 14:03:06,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg57e9c4ac-417a-4456-8ece-7eba6231384f/GCF_000423005.1_ASM42300v1_genomic.fna.gz | prodigal -d GCF_000423005.1_ASM42300v1_genomic.fna/cds.fna -a GCF_000423005.1_ASM42300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:25,746] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:25,747] [INFO] Task started: HMMsearch
[2024-01-24 14:03:25,747] [INFO] Running command: hmmsearch --tblout GCF_000423005.1_ASM42300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6d33683-d76a-4074-b53e-16822c07c7d4/dqc_reference/reference_markers.hmm GCF_000423005.1_ASM42300v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:26,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:26,081] [INFO] Found 6/6 markers.
[2024-01-24 14:03:26,123] [INFO] Query marker FASTA was written to GCF_000423005.1_ASM42300v1_genomic.fna/markers.fasta
[2024-01-24 14:03:26,123] [INFO] Task started: Blastn
[2024-01-24 14:03:26,124] [INFO] Running command: blastn -query GCF_000423005.1_ASM42300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6d33683-d76a-4074-b53e-16822c07c7d4/dqc_reference/reference_markers.fasta -out GCF_000423005.1_ASM42300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:26,814] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:26,817] [INFO] Selected 13 target genomes.
[2024-01-24 14:03:26,818] [INFO] Target genome list was writen to GCF_000423005.1_ASM42300v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:26,824] [INFO] Task started: fastANI
[2024-01-24 14:03:26,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e9c4ac-417a-4456-8ece-7eba6231384f/GCF_000423005.1_ASM42300v1_genomic.fna.gz --refList GCF_000423005.1_ASM42300v1_genomic.fna/target_genomes.txt --output GCF_000423005.1_ASM42300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:39,061] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:39,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6d33683-d76a-4074-b53e-16822c07c7d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:39,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6d33683-d76a-4074-b53e-16822c07c7d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:39,077] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:39,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:39,078] [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 mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	100.0	1451	1452	95	conclusive
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	81.1036	875	1452	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	80.9366	847	1452	95	below_threshold
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	80.6432	801	1452	95	below_threshold
Gelidibacter maritimus	strain=F6074	GCA_014062315.1	2761487	2761487	type	True	79.9864	768	1452	95	below_threshold
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	79.481	639	1452	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	79.4396	656	1452	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	78.9502	549	1452	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.8199	150	1452	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.7656	118	1452	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.6785	107	1452	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.6137	120	1452	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5944	150	1452	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:39,079] [INFO] DFAST Taxonomy check result was written to GCF_000423005.1_ASM42300v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:39,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:39,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:39,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6d33683-d76a-4074-b53e-16822c07c7d4/dqc_reference/checkm_data
[2024-01-24 14:03:39,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:39,129] [INFO] Task started: CheckM
[2024-01-24 14:03:39,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423005.1_ASM42300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423005.1_ASM42300v1_genomic.fna/checkm_input GCF_000423005.1_ASM42300v1_genomic.fna/checkm_result
[2024-01-24 14:04:34,455] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:34,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:34,480] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:34,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:34,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423005.1_ASM42300v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:34,482] [INFO] Task started: Blastn
[2024-01-24 14:04:34,482] [INFO] Running command: blastn -query GCF_000423005.1_ASM42300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6d33683-d76a-4074-b53e-16822c07c7d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423005.1_ASM42300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:35,388] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:35,392] [INFO] Selected 8 target genomes.
[2024-01-24 14:04:35,392] [INFO] Target genome list was writen to GCF_000423005.1_ASM42300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:35,402] [INFO] Task started: fastANI
[2024-01-24 14:04:35,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e9c4ac-417a-4456-8ece-7eba6231384f/GCF_000423005.1_ASM42300v1_genomic.fna.gz --refList GCF_000423005.1_ASM42300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423005.1_ASM42300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:43,316] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:43,324] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:43,324] [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_000423005.1	s__Gelidibacter mesophilus	100.0	1451	1452	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_017581925.1	s__Gelidibacter sp017581925	81.1113	874	1452	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	80.9368	847	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725055.1	s__Gelidibacter japonicus	80.6237	804	1452	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	79.9677	771	1452	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	79.4753	639	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCF_016469035.1	s__Gelidibacter salicanalis_A	79.4275	640	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997285.1	s__Gelidibacter salicanalis	78.9548	549	1452	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 14:04:43,326] [INFO] GTDB search result was written to GCF_000423005.1_ASM42300v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:43,326] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:43,330] [INFO] DFAST_QC result json was written to GCF_000423005.1_ASM42300v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:43,330] [INFO] DFAST_QC completed!
[2024-01-24 14:04:43,330] [INFO] Total running time: 0h1m39s