[2023-03-17 23:00:49,596] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:00:49,596] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:00:49,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f92fbee-03fc-4fc9-957d-b65dd36f4801/dqc_reference
[2023-03-17 23:00:52,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:00:52,224] [INFO] Task started: Prodigal
[2023-03-17 23:00:52,224] [INFO] Running command: cat /var/lib/cwl/stg9bce2fc2-7454-4d26-afac-bac002701feb/OceanDNA-b7189.fa | prodigal -d OceanDNA-b7189/cds.fna -a OceanDNA-b7189/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:01:13,694] [INFO] Task succeeded: Prodigal
[2023-03-17 23:01:13,694] [INFO] Task started: HMMsearch
[2023-03-17 23:01:13,694] [INFO] Running command: hmmsearch --tblout OceanDNA-b7189/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f92fbee-03fc-4fc9-957d-b65dd36f4801/dqc_reference/reference_markers.hmm OceanDNA-b7189/protein.faa > /dev/null
[2023-03-17 23:01:13,903] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:01:13,904] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9bce2fc2-7454-4d26-afac-bac002701feb/OceanDNA-b7189.fa]
[2023-03-17 23:01:13,924] [INFO] Query marker FASTA was written to OceanDNA-b7189/markers.fasta
[2023-03-17 23:01:13,925] [INFO] Task started: Blastn
[2023-03-17 23:01:13,925] [INFO] Running command: blastn -query OceanDNA-b7189/markers.fasta -db /var/lib/cwl/stg0f92fbee-03fc-4fc9-957d-b65dd36f4801/dqc_reference/reference_markers.fasta -out OceanDNA-b7189/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:01:14,484] [INFO] Task succeeded: Blastn
[2023-03-17 23:01:14,485] [INFO] Selected 19 target genomes.
[2023-03-17 23:01:14,485] [INFO] Target genome list was writen to OceanDNA-b7189/target_genomes.txt
[2023-03-17 23:01:14,495] [INFO] Task started: fastANI
[2023-03-17 23:01:14,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bce2fc2-7454-4d26-afac-bac002701feb/OceanDNA-b7189.fa --refList OceanDNA-b7189/target_genomes.txt --output OceanDNA-b7189/fastani_result.tsv --threads 1
[2023-03-17 23:01:26,647] [INFO] Task succeeded: fastANI
[2023-03-17 23:01:26,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f92fbee-03fc-4fc9-957d-b65dd36f4801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:01:26,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f92fbee-03fc-4fc9-957d-b65dd36f4801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:01:26,657] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:01:26,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:01:26,657] [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
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	88.1787	843	1031	95	below_threshold
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	78.232	326	1031	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	78.006	306	1031	95	below_threshold
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	77.4701	186	1031	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	77.271	201	1031	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	76.763	170	1031	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	76.7516	120	1031	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	76.7049	126	1031	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	76.5094	105	1031	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	76.5012	139	1031	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	76.4653	173	1031	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	76.4462	173	1031	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:01:26,657] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7189/tc_result.tsv
[2023-03-17 23:01:26,657] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:01:26,657] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:01:26,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f92fbee-03fc-4fc9-957d-b65dd36f4801/dqc_reference/checkm_data
[2023-03-17 23:01:26,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:01:26,662] [INFO] Task started: CheckM
[2023-03-17 23:01:26,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7189/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7189/checkm_input OceanDNA-b7189/checkm_result
[2023-03-17 23:02:22,109] [INFO] Task succeeded: CheckM
[2023-03-17 23:02:22,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:02:22,114] [INFO] ===== Completeness check finished =====
[2023-03-17 23:02:22,114] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:02:22,114] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7189/markers.fasta)
[2023-03-17 23:02:22,115] [INFO] Task started: Blastn
[2023-03-17 23:02:22,115] [INFO] Running command: blastn -query OceanDNA-b7189/markers.fasta -db /var/lib/cwl/stg0f92fbee-03fc-4fc9-957d-b65dd36f4801/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7189/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:02:22,890] [INFO] Task succeeded: Blastn
[2023-03-17 23:02:22,891] [INFO] Selected 14 target genomes.
[2023-03-17 23:02:22,891] [INFO] Target genome list was writen to OceanDNA-b7189/target_genomes_gtdb.txt
[2023-03-17 23:02:22,907] [INFO] Task started: fastANI
[2023-03-17 23:02:22,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bce2fc2-7454-4d26-afac-bac002701feb/OceanDNA-b7189.fa --refList OceanDNA-b7189/target_genomes_gtdb.txt --output OceanDNA-b7189/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:02:31,264] [INFO] Task succeeded: fastANI
[2023-03-17 23:02:31,272] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:02:31,272] [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_007993795.1	s__Gillisia arcticum	88.1787	843	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006159205.1	s__Gillisia flava	78.232	326	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243235.1	s__Gillisia limnaea	78.006	306	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104765.1	s__Gillisia sp900104765	77.6357	185	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_000403785.1	s__Gillisia sp000403785	77.5664	175	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649785.1	s__Gillisia sp016649785	77.5238	154	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	77.2702	202	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012038135.1	s__Salinimicrobium sp012038135	77.0572	139	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	76.8078	130	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745315.1	s__Salegentibacter sp000745315	76.7686	161	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651535.1	s__Salinimicrobium marinum	76.7655	171	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	76.7516	120	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016236915.1	s__Salegentibacter maritimus	76.5165	138	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_900112105.1	s__Zunongwangia mangrovi	76.5094	105	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:02:31,273] [INFO] GTDB search result was written to OceanDNA-b7189/result_gtdb.tsv
[2023-03-17 23:02:31,273] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:02:31,275] [INFO] DFAST_QC result json was written to OceanDNA-b7189/dqc_result.json
[2023-03-17 23:02:31,275] [INFO] DFAST_QC completed!
[2023-03-17 23:02:31,275] [INFO] Total running time: 0h1m42s