[2024-01-24 12:44:33,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:33,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:33,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgb86b73ed-35ae-4279-b407-727db85de4ea/dqc_reference
[2024-01-24 12:44:34,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:34,603] [INFO] Task started: Prodigal
[2024-01-24 12:44:34,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ca97cc2-4012-46d2-87d7-e1867fa4af88/GCF_017051705.1_ASM1705170v1_genomic.fna.gz | prodigal -d GCF_017051705.1_ASM1705170v1_genomic.fna/cds.fna -a GCF_017051705.1_ASM1705170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:54,754] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:54,754] [INFO] Task started: HMMsearch
[2024-01-24 12:44:54,754] [INFO] Running command: hmmsearch --tblout GCF_017051705.1_ASM1705170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb86b73ed-35ae-4279-b407-727db85de4ea/dqc_reference/reference_markers.hmm GCF_017051705.1_ASM1705170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:54,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:54,989] [INFO] Found 6/6 markers.
[2024-01-24 12:44:55,028] [INFO] Query marker FASTA was written to GCF_017051705.1_ASM1705170v1_genomic.fna/markers.fasta
[2024-01-24 12:44:55,028] [INFO] Task started: Blastn
[2024-01-24 12:44:55,029] [INFO] Running command: blastn -query GCF_017051705.1_ASM1705170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb86b73ed-35ae-4279-b407-727db85de4ea/dqc_reference/reference_markers.fasta -out GCF_017051705.1_ASM1705170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,609] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,613] [INFO] Selected 14 target genomes.
[2024-01-24 12:44:55,613] [INFO] Target genome list was writen to GCF_017051705.1_ASM1705170v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,638] [INFO] Task started: fastANI
[2024-01-24 12:44:55,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca97cc2-4012-46d2-87d7-e1867fa4af88/GCF_017051705.1_ASM1705170v1_genomic.fna.gz --refList GCF_017051705.1_ASM1705170v1_genomic.fna/target_genomes.txt --output GCF_017051705.1_ASM1705170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:07,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:07,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb86b73ed-35ae-4279-b407-727db85de4ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:07,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb86b73ed-35ae-4279-b407-727db85de4ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:07,997] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:07,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:07,998] [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
Algoriphagus lutimaris	strain=KCTC 22630	GCA_017051705.1	613197	613197	type	True	100.0	1564	1564	95	conclusive
Algoriphagus halophilus	strain=DSM 15292	GCA_900129785.1	226505	226505	type	True	90.9774	1400	1564	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	79.8941	676	1564	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	79.8756	658	1564	95	below_threshold
Algoriphagus machipongonensis	strain=PR1	GCA_000166275.1	388413	388413	type	True	78.8498	573	1564	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	77.8114	242	1564	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	77.6732	301	1564	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	77.6542	270	1564	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	77.4402	302	1564	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	77.2249	265	1564	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.8453	95	1564	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	76.1441	50	1564	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	76.0357	51	1564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:08,000] [INFO] DFAST Taxonomy check result was written to GCF_017051705.1_ASM1705170v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:08,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:08,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:08,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb86b73ed-35ae-4279-b407-727db85de4ea/dqc_reference/checkm_data
[2024-01-24 12:45:08,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:08,046] [INFO] Task started: CheckM
[2024-01-24 12:45:08,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017051705.1_ASM1705170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017051705.1_ASM1705170v1_genomic.fna/checkm_input GCF_017051705.1_ASM1705170v1_genomic.fna/checkm_result
[2024-01-24 12:46:05,589] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:05,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:05,609] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:05,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:05,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017051705.1_ASM1705170v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:05,610] [INFO] Task started: Blastn
[2024-01-24 12:46:05,610] [INFO] Running command: blastn -query GCF_017051705.1_ASM1705170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb86b73ed-35ae-4279-b407-727db85de4ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_017051705.1_ASM1705170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:06,340] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:06,344] [INFO] Selected 9 target genomes.
[2024-01-24 12:46:06,344] [INFO] Target genome list was writen to GCF_017051705.1_ASM1705170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:06,371] [INFO] Task started: fastANI
[2024-01-24 12:46:06,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca97cc2-4012-46d2-87d7-e1867fa4af88/GCF_017051705.1_ASM1705170v1_genomic.fna.gz --refList GCF_017051705.1_ASM1705170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017051705.1_ASM1705170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:14,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:14,644] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:14,644] [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_017051705.1	s__Algoriphagus lutimaris	100.0	1564	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129785.1	s__Algoriphagus halophilus	90.9774	1400	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014206875.1	s__Algoriphagus iocasae	79.8942	676	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	79.8707	659	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	78.8604	571	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	77.6653	301	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	77.6542	270	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	77.4539	302	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	77.2202	264	1564	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:14,646] [INFO] GTDB search result was written to GCF_017051705.1_ASM1705170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:14,647] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:14,650] [INFO] DFAST_QC result json was written to GCF_017051705.1_ASM1705170v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:14,650] [INFO] DFAST_QC completed!
[2024-01-24 12:46:14,650] [INFO] Total running time: 0h1m41s