[2024-01-25 20:12:20,532] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:20,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:20,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg10233da2-0c3f-4c44-9723-917d5df1227e/dqc_reference
[2024-01-25 20:12:21,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:21,705] [INFO] Task started: Prodigal
[2024-01-25 20:12:21,706] [INFO] Running command: gunzip -c /var/lib/cwl/stga658009e-d608-47e3-aded-acb06e696678/GCF_001005315.1_ASM100531v1_genomic.fna.gz | prodigal -d GCF_001005315.1_ASM100531v1_genomic.fna/cds.fna -a GCF_001005315.1_ASM100531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:39,061] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:39,061] [INFO] Task started: HMMsearch
[2024-01-25 20:12:39,061] [INFO] Running command: hmmsearch --tblout GCF_001005315.1_ASM100531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10233da2-0c3f-4c44-9723-917d5df1227e/dqc_reference/reference_markers.hmm GCF_001005315.1_ASM100531v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:39,335] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:39,336] [INFO] Found 6/6 markers.
[2024-01-25 20:12:39,378] [INFO] Query marker FASTA was written to GCF_001005315.1_ASM100531v1_genomic.fna/markers.fasta
[2024-01-25 20:12:39,378] [INFO] Task started: Blastn
[2024-01-25 20:12:39,378] [INFO] Running command: blastn -query GCF_001005315.1_ASM100531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10233da2-0c3f-4c44-9723-917d5df1227e/dqc_reference/reference_markers.fasta -out GCF_001005315.1_ASM100531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:40,024] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:40,026] [INFO] Selected 11 target genomes.
[2024-01-25 20:12:40,027] [INFO] Target genome list was writen to GCF_001005315.1_ASM100531v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:40,033] [INFO] Task started: fastANI
[2024-01-25 20:12:40,034] [INFO] Running command: fastANI --query /var/lib/cwl/stga658009e-d608-47e3-aded-acb06e696678/GCF_001005315.1_ASM100531v1_genomic.fna.gz --refList GCF_001005315.1_ASM100531v1_genomic.fna/target_genomes.txt --output GCF_001005315.1_ASM100531v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:50,790] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:50,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10233da2-0c3f-4c44-9723-917d5df1227e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:50,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10233da2-0c3f-4c44-9723-917d5df1227e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:50,798] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:50,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:50,798] [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
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	100.0	1691	1699	95	conclusive
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	81.4507	958	1699	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	81.4464	978	1699	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	81.1575	922	1699	95	below_threshold
Kordia periserrulae	strain=DSM 25731	GCA_003054265.1	701523	701523	type	True	79.7208	830	1699	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	79.2414	625	1699	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8616	117	1699	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.667	115	1699	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.4564	125	1699	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	75.8068	87	1699	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	75.4819	61	1699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:50,800] [INFO] DFAST Taxonomy check result was written to GCF_001005315.1_ASM100531v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:50,800] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:50,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:50,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10233da2-0c3f-4c44-9723-917d5df1227e/dqc_reference/checkm_data
[2024-01-25 20:12:50,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:50,854] [INFO] Task started: CheckM
[2024-01-25 20:12:50,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001005315.1_ASM100531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001005315.1_ASM100531v1_genomic.fna/checkm_input GCF_001005315.1_ASM100531v1_genomic.fna/checkm_result
[2024-01-25 20:13:42,908] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:42,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:42,982] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:42,982] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:42,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001005315.1_ASM100531v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:42,983] [INFO] Task started: Blastn
[2024-01-25 20:13:42,983] [INFO] Running command: blastn -query GCF_001005315.1_ASM100531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10233da2-0c3f-4c44-9723-917d5df1227e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001005315.1_ASM100531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:43,956] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:43,959] [INFO] Selected 6 target genomes.
[2024-01-25 20:13:43,959] [INFO] Target genome list was writen to GCF_001005315.1_ASM100531v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:43,970] [INFO] Task started: fastANI
[2024-01-25 20:13:43,970] [INFO] Running command: fastANI --query /var/lib/cwl/stga658009e-d608-47e3-aded-acb06e696678/GCF_001005315.1_ASM100531v1_genomic.fna.gz --refList GCF_001005315.1_ASM100531v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001005315.1_ASM100531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:52,359] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:52,365] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:52,365] [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_001005315.1	s__Kordia jejudonensis	100.0	1691	1699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000154725.1	s__Kordia algicida	81.4536	956	1699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397005.1	s__Kordia aestuariivivens	81.4296	981	1699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901525.1	s__Kordia antarctica	81.1661	921	1699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352465.1	s__Kordia sp003352465	80.5878	951	1699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006383075.2	s__Kordia sp006383075	79.8395	796	1699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:52,367] [INFO] GTDB search result was written to GCF_001005315.1_ASM100531v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:52,368] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:52,370] [INFO] DFAST_QC result json was written to GCF_001005315.1_ASM100531v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:52,370] [INFO] DFAST_QC completed!
[2024-01-25 20:13:52,370] [INFO] Total running time: 0h1m32s