[2023-03-14 14:05:20,205] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:05:20,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:05:20,205] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4003b1a-be15-468b-9cf1-936cd15dc06c/dqc_reference
[2023-03-14 14:05:21,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:05:21,366] [INFO] Task started: Prodigal
[2023-03-14 14:05:21,366] [INFO] Running command: cat /var/lib/cwl/stg6e860be5-2052-4297-828e-17938c535be0/OceanDNA-b6841.fa | prodigal -d OceanDNA-b6841/cds.fna -a OceanDNA-b6841/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:05:35,081] [INFO] Task succeeded: Prodigal
[2023-03-14 14:05:35,082] [INFO] Task started: HMMsearch
[2023-03-14 14:05:35,082] [INFO] Running command: hmmsearch --tblout OceanDNA-b6841/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4003b1a-be15-468b-9cf1-936cd15dc06c/dqc_reference/reference_markers.hmm OceanDNA-b6841/protein.faa > /dev/null
[2023-03-14 14:05:35,252] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:05:35,253] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6e860be5-2052-4297-828e-17938c535be0/OceanDNA-b6841.fa]
[2023-03-14 14:05:35,267] [INFO] Query marker FASTA was written to OceanDNA-b6841/markers.fasta
[2023-03-14 14:05:35,268] [INFO] Task started: Blastn
[2023-03-14 14:05:35,269] [INFO] Running command: blastn -query OceanDNA-b6841/markers.fasta -db /var/lib/cwl/stgc4003b1a-be15-468b-9cf1-936cd15dc06c/dqc_reference/reference_markers.fasta -out OceanDNA-b6841/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:05:35,910] [INFO] Task succeeded: Blastn
[2023-03-14 14:05:35,911] [INFO] Selected 13 target genomes.
[2023-03-14 14:05:35,911] [INFO] Target genome list was writen to OceanDNA-b6841/target_genomes.txt
[2023-03-14 14:05:35,918] [INFO] Task started: fastANI
[2023-03-14 14:05:35,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e860be5-2052-4297-828e-17938c535be0/OceanDNA-b6841.fa --refList OceanDNA-b6841/target_genomes.txt --output OceanDNA-b6841/fastani_result.tsv --threads 1
[2023-03-14 14:05:43,850] [INFO] Task succeeded: fastANI
[2023-03-14 14:05:43,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4003b1a-be15-468b-9cf1-936cd15dc06c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:05:43,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4003b1a-be15-468b-9cf1-936cd15dc06c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:05:43,859] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:05:43,859] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:05:43,859] [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
Flavobacterium arcticum	strain=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	81.0491	508	769	95	below_threshold
Flavobacterium arcticum	strain=SM1502	GCA_003344925.1	1784713	1784713	type	True	80.9941	513	769	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	79.3703	428	769	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	79.1573	401	769	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	79.1035	398	769	95	below_threshold
Flavobacterium suaedae	strain=CGMCC 1.15461	GCA_014642915.1	1767027	1767027	type	True	78.4941	334	769	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	77.0196	93	769	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	76.9564	94	769	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	76.8714	93	769	95	below_threshold
Flavobacterium piscinae	strain=ICH-30	GCA_004122145.1	2506424	2506424	type	True	76.8086	70	769	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.6715	67	769	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.1909	61	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:05:43,859] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6841/tc_result.tsv
[2023-03-14 14:05:43,859] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:05:43,859] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:05:43,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4003b1a-be15-468b-9cf1-936cd15dc06c/dqc_reference/checkm_data
[2023-03-14 14:05:43,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:05:43,863] [INFO] Task started: CheckM
[2023-03-14 14:05:43,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6841/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6841/checkm_input OceanDNA-b6841/checkm_result
[2023-03-14 14:06:34,020] [INFO] Task succeeded: CheckM
[2023-03-14 14:06:34,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:06:34,022] [INFO] ===== Completeness check finished =====
[2023-03-14 14:06:34,023] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:06:34,023] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6841/markers.fasta)
[2023-03-14 14:06:34,023] [INFO] Task started: Blastn
[2023-03-14 14:06:34,023] [INFO] Running command: blastn -query OceanDNA-b6841/markers.fasta -db /var/lib/cwl/stgc4003b1a-be15-468b-9cf1-936cd15dc06c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6841/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:06:35,042] [INFO] Task succeeded: Blastn
[2023-03-14 14:06:35,042] [INFO] Selected 15 target genomes.
[2023-03-14 14:06:35,043] [INFO] Target genome list was writen to OceanDNA-b6841/target_genomes_gtdb.txt
[2023-03-14 14:06:35,054] [INFO] Task started: fastANI
[2023-03-14 14:06:35,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e860be5-2052-4297-828e-17938c535be0/OceanDNA-b6841.fa --refList OceanDNA-b6841/target_genomes_gtdb.txt --output OceanDNA-b6841/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:06:46,649] [INFO] Task succeeded: fastANI
[2023-03-14 14:06:46,658] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:06:46,658] [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
GCA_001874325.1	s__Flavobacterium sp001874325	99.9855	669	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003344925.1	s__Flavobacterium arcticum	80.9941	513	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004634195.1	s__Flavobacterium sp004634195	79.1035	398	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
GCF_014642915.1	s__Flavobacterium suaedae	78.4993	333	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	77.859	188	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003403075.1	s__Flavobacterium sp003403075	77.6766	133	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826935.1	s__Flavobacterium sp009826935	77.6569	132	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	77.5849	191	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097145.1	s__Flavobacterium sp007097145	77.2862	151	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	77.0529	102	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422705.1	s__Flavobacterium soli	77.0196	93	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014305155.1	s__Flavobacterium sp014305155	76.9899	108	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014642275.1	s__Flavobacterium lutivivi	76.8985	92	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122145.1	s__Flavobacterium piscinae	76.8786	67	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
GCF_003865405.1	s__Flavobacterium tangerinum	76.8405	80	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:06:46,664] [INFO] GTDB search result was written to OceanDNA-b6841/result_gtdb.tsv
[2023-03-14 14:06:46,665] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:06:46,666] [INFO] DFAST_QC result json was written to OceanDNA-b6841/dqc_result.json
[2023-03-14 14:06:46,666] [INFO] DFAST_QC completed!
[2023-03-14 14:06:46,666] [INFO] Total running time: 0h1m26s