[2023-03-19 03:22:59,901] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,902] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg409a31ad-d690-46e2-af4f-4e9fea700069/dqc_reference
[2023-03-19 03:23:01,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:01,002] [INFO] Task started: Prodigal
[2023-03-19 03:23:01,002] [INFO] Running command: cat /var/lib/cwl/stg71b279b1-b715-4317-9ca4-02fac6a2721b/OceanDNA-b8213.fa | prodigal -d OceanDNA-b8213/cds.fna -a OceanDNA-b8213/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:06,710] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:06,710] [INFO] Task started: HMMsearch
[2023-03-19 03:23:06,710] [INFO] Running command: hmmsearch --tblout OceanDNA-b8213/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg409a31ad-d690-46e2-af4f-4e9fea700069/dqc_reference/reference_markers.hmm OceanDNA-b8213/protein.faa > /dev/null
[2023-03-19 03:23:06,904] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:06,905] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg71b279b1-b715-4317-9ca4-02fac6a2721b/OceanDNA-b8213.fa]
[2023-03-19 03:23:06,930] [INFO] Query marker FASTA was written to OceanDNA-b8213/markers.fasta
[2023-03-19 03:23:06,931] [INFO] Task started: Blastn
[2023-03-19 03:23:06,931] [INFO] Running command: blastn -query OceanDNA-b8213/markers.fasta -db /var/lib/cwl/stg409a31ad-d690-46e2-af4f-4e9fea700069/dqc_reference/reference_markers.fasta -out OceanDNA-b8213/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:07,508] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:07,514] [INFO] Selected 22 target genomes.
[2023-03-19 03:23:07,515] [INFO] Target genome list was writen to OceanDNA-b8213/target_genomes.txt
[2023-03-19 03:23:07,526] [INFO] Task started: fastANI
[2023-03-19 03:23:07,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b279b1-b715-4317-9ca4-02fac6a2721b/OceanDNA-b8213.fa --refList OceanDNA-b8213/target_genomes.txt --output OceanDNA-b8213/fastani_result.tsv --threads 1
[2023-03-19 03:23:20,327] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:20,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg409a31ad-d690-46e2-af4f-4e9fea700069/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:20,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg409a31ad-d690-46e2-af4f-4e9fea700069/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:20,328] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:20,328] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:23:20,328] [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
--------------------------------------------------------------------------------
[2023-03-19 03:23:20,335] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8213/tc_result.tsv
[2023-03-19 03:23:20,347] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:20,347] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:20,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg409a31ad-d690-46e2-af4f-4e9fea700069/dqc_reference/checkm_data
[2023-03-19 03:23:20,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:20,368] [INFO] Task started: CheckM
[2023-03-19 03:23:20,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8213/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8213/checkm_input OceanDNA-b8213/checkm_result
[2023-03-19 03:23:40,306] [INFO] Task succeeded: CheckM
[2023-03-19 03:23:40,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:23:40,335] [INFO] ===== Completeness check finished =====
[2023-03-19 03:23:40,335] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:23:40,335] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8213/markers.fasta)
[2023-03-19 03:23:40,337] [INFO] Task started: Blastn
[2023-03-19 03:23:40,337] [INFO] Running command: blastn -query OceanDNA-b8213/markers.fasta -db /var/lib/cwl/stg409a31ad-d690-46e2-af4f-4e9fea700069/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8213/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:41,282] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:41,288] [INFO] Selected 10 target genomes.
[2023-03-19 03:23:41,288] [INFO] Target genome list was writen to OceanDNA-b8213/target_genomes_gtdb.txt
[2023-03-19 03:23:41,345] [INFO] Task started: fastANI
[2023-03-19 03:23:41,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b279b1-b715-4317-9ca4-02fac6a2721b/OceanDNA-b8213.fa --refList OceanDNA-b8213/target_genomes_gtdb.txt --output OceanDNA-b8213/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:23:44,152] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:44,158] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:23:44,158] [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_003331265.1	s__MAG-121220-bin8 sp003331265	80.6915	204	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	80.6054	231	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	79.1931	181	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	79.0061	145	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	78.9566	183	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	78.1713	138	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	77.939	153	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	77.5068	104	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	76.7166	93	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
--------------------------------------------------------------------------------
[2023-03-19 03:23:44,160] [INFO] GTDB search result was written to OceanDNA-b8213/result_gtdb.tsv
[2023-03-19 03:23:44,161] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:23:44,166] [INFO] DFAST_QC result json was written to OceanDNA-b8213/dqc_result.json
[2023-03-19 03:23:44,166] [INFO] DFAST_QC completed!
[2023-03-19 03:23:44,166] [INFO] Total running time: 0h0m44s