[2023-03-18 02:27:59,050] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:59,050] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:59,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgb65caabc-2e88-4b8e-bd98-ee4733b9d488/dqc_reference
[2023-03-18 02:28:00,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:28:00,143] [INFO] Task started: Prodigal
[2023-03-18 02:28:00,144] [INFO] Running command: cat /var/lib/cwl/stg5ea2fb68-852d-4139-a0c9-808595c34939/OceanDNA-b8711.fa | prodigal -d OceanDNA-b8711/cds.fna -a OceanDNA-b8711/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:04,424] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:04,424] [INFO] Task started: HMMsearch
[2023-03-18 02:28:04,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b8711/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb65caabc-2e88-4b8e-bd98-ee4733b9d488/dqc_reference/reference_markers.hmm OceanDNA-b8711/protein.faa > /dev/null
[2023-03-18 02:28:04,606] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:04,606] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5ea2fb68-852d-4139-a0c9-808595c34939/OceanDNA-b8711.fa]
[2023-03-18 02:28:04,614] [INFO] Query marker FASTA was written to OceanDNA-b8711/markers.fasta
[2023-03-18 02:28:04,615] [INFO] Task started: Blastn
[2023-03-18 02:28:04,616] [INFO] Running command: blastn -query OceanDNA-b8711/markers.fasta -db /var/lib/cwl/stgb65caabc-2e88-4b8e-bd98-ee4733b9d488/dqc_reference/reference_markers.fasta -out OceanDNA-b8711/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:05,202] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:05,203] [INFO] Selected 31 target genomes.
[2023-03-18 02:28:05,203] [INFO] Target genome list was writen to OceanDNA-b8711/target_genomes.txt
[2023-03-18 02:28:05,219] [INFO] Task started: fastANI
[2023-03-18 02:28:05,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea2fb68-852d-4139-a0c9-808595c34939/OceanDNA-b8711.fa --refList OceanDNA-b8711/target_genomes.txt --output OceanDNA-b8711/fastani_result.tsv --threads 1
[2023-03-18 02:28:20,481] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:20,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb65caabc-2e88-4b8e-bd98-ee4733b9d488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:20,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb65caabc-2e88-4b8e-bd98-ee4733b9d488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:20,482] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:20,482] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:28:20,482] [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
--------------------------------------------------------------------------------
[2023-03-18 02:28:20,482] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8711/tc_result.tsv
[2023-03-18 02:28:20,483] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:20,483] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:20,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb65caabc-2e88-4b8e-bd98-ee4733b9d488/dqc_reference/checkm_data
[2023-03-18 02:28:20,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:20,487] [INFO] Task started: CheckM
[2023-03-18 02:28:20,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8711/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8711/checkm_input OceanDNA-b8711/checkm_result
[2023-03-18 02:28:37,235] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:37,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:37,237] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:37,237] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:37,237] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8711/markers.fasta)
[2023-03-18 02:28:37,237] [INFO] Task started: Blastn
[2023-03-18 02:28:37,237] [INFO] Running command: blastn -query OceanDNA-b8711/markers.fasta -db /var/lib/cwl/stgb65caabc-2e88-4b8e-bd98-ee4733b9d488/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8711/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:37,988] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:37,989] [INFO] Selected 16 target genomes.
[2023-03-18 02:28:37,989] [INFO] Target genome list was writen to OceanDNA-b8711/target_genomes_gtdb.txt
[2023-03-18 02:28:38,020] [INFO] Task started: fastANI
[2023-03-18 02:28:38,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea2fb68-852d-4139-a0c9-808595c34939/OceanDNA-b8711.fa --refList OceanDNA-b8711/target_genomes_gtdb.txt --output OceanDNA-b8711/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:41,352] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:41,362] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:28:41,362] [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_002697255.1	s__MED-G13 sp002697255	79.9199	145	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560045.1	s__MED-G13 sp902560045	79.9044	114	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.04	98.52	0.67	0.66	3	-
GCA_902510475.1	s__MED-G13 sp902510475	79.8434	111	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557655.1	s__MED-G13 sp902557655	79.7678	135	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.84	99.84	0.82	0.82	2	-
GCA_902509675.1	s__MED-G13 sp902509675	78.8085	96	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	78.1004	108	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902604715.1	s__MED-G13 sp902604715	77.9592	96	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902519075.1	s__MED-G13 sp902519075	77.8754	92	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626365.1	s__MED-G13 sp902626365	77.8582	97	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCA_902517895.1	s__MED-G13 sp902517895	77.7976	89	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081325.1	s__MED-G13 sp008081325	77.7722	75	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702745.1	s__MED-G13 sp002702745	77.7368	91	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626585.1	s__MED-G13 sp902626585	77.6404	105	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526075.1	s__MED-G13 sp902526075	77.6248	85	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902581145.1	s__MED-G13 sp902581145	77.3805	102	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518355.1	s__MED-G13 sp902518355	77.3662	106	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:41,362] [INFO] GTDB search result was written to OceanDNA-b8711/result_gtdb.tsv
[2023-03-18 02:28:41,362] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:41,363] [INFO] DFAST_QC result json was written to OceanDNA-b8711/dqc_result.json
[2023-03-18 02:28:41,363] [INFO] DFAST_QC completed!
[2023-03-18 02:28:41,363] [INFO] Total running time: 0h0m42s