[2023-03-15 07:49:00,151] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:49:00,155] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:49:00,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg24a7b403-2cce-4cda-84ee-c07eb7417eb2/dqc_reference
[2023-03-15 07:49:01,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:49:01,243] [INFO] Task started: Prodigal
[2023-03-15 07:49:01,243] [INFO] Running command: cat /var/lib/cwl/stg3ee4c8f3-04b3-4401-88fb-acfd4ab77a53/OceanDNA-b6302.fa | prodigal -d OceanDNA-b6302/cds.fna -a OceanDNA-b6302/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:49:08,021] [INFO] Task succeeded: Prodigal
[2023-03-15 07:49:08,021] [INFO] Task started: HMMsearch
[2023-03-15 07:49:08,021] [INFO] Running command: hmmsearch --tblout OceanDNA-b6302/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24a7b403-2cce-4cda-84ee-c07eb7417eb2/dqc_reference/reference_markers.hmm OceanDNA-b6302/protein.faa > /dev/null
[2023-03-15 07:49:08,197] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:49:08,197] [INFO] Found 6/6 markers.
[2023-03-15 07:49:08,239] [INFO] Query marker FASTA was written to OceanDNA-b6302/markers.fasta
[2023-03-15 07:49:08,239] [INFO] Task started: Blastn
[2023-03-15 07:49:08,239] [INFO] Running command: blastn -query OceanDNA-b6302/markers.fasta -db /var/lib/cwl/stg24a7b403-2cce-4cda-84ee-c07eb7417eb2/dqc_reference/reference_markers.fasta -out OceanDNA-b6302/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:49:08,784] [INFO] Task succeeded: Blastn
[2023-03-15 07:49:08,801] [INFO] Selected 26 target genomes.
[2023-03-15 07:49:08,801] [INFO] Target genome list was writen to OceanDNA-b6302/target_genomes.txt
[2023-03-15 07:49:08,813] [INFO] Task started: fastANI
[2023-03-15 07:49:08,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ee4c8f3-04b3-4401-88fb-acfd4ab77a53/OceanDNA-b6302.fa --refList OceanDNA-b6302/target_genomes.txt --output OceanDNA-b6302/fastani_result.tsv --threads 1
[2023-03-15 07:49:23,171] [INFO] Task succeeded: fastANI
[2023-03-15 07:49:23,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24a7b403-2cce-4cda-84ee-c07eb7417eb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:49:23,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24a7b403-2cce-4cda-84ee-c07eb7417eb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:49:23,177] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:49:23,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:49:23,177] [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
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.0507	51	383	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.0507	51	383	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	75.8918	53	383	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	75.8201	51	383	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	75.3124	56	383	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:49:23,187] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6302/tc_result.tsv
[2023-03-15 07:49:23,201] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:49:23,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:49:23,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24a7b403-2cce-4cda-84ee-c07eb7417eb2/dqc_reference/checkm_data
[2023-03-15 07:49:23,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:49:23,210] [INFO] Task started: CheckM
[2023-03-15 07:49:23,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6302/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6302/checkm_input OceanDNA-b6302/checkm_result
[2023-03-15 07:49:45,931] [INFO] Task succeeded: CheckM
[2023-03-15 07:49:45,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:49:45,989] [INFO] ===== Completeness check finished =====
[2023-03-15 07:49:45,989] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:49:45,990] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6302/markers.fasta)
[2023-03-15 07:49:45,990] [INFO] Task started: Blastn
[2023-03-15 07:49:45,990] [INFO] Running command: blastn -query OceanDNA-b6302/markers.fasta -db /var/lib/cwl/stg24a7b403-2cce-4cda-84ee-c07eb7417eb2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6302/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:49:46,749] [INFO] Task succeeded: Blastn
[2023-03-15 07:49:46,760] [INFO] Selected 15 target genomes.
[2023-03-15 07:49:46,760] [INFO] Target genome list was writen to OceanDNA-b6302/target_genomes_gtdb.txt
[2023-03-15 07:49:46,777] [INFO] Task started: fastANI
[2023-03-15 07:49:46,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ee4c8f3-04b3-4401-88fb-acfd4ab77a53/OceanDNA-b6302.fa --refList OceanDNA-b6302/target_genomes_gtdb.txt --output OceanDNA-b6302/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:49:50,916] [INFO] Task succeeded: fastANI
[2023-03-15 07:49:50,922] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:49:50,922] [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_902515565.1	s__SGZJ01 sp902515565	86.9936	254	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213995.1	s__SGZJ01 sp004213995	86.7117	285	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	95.83	95.53	0.71	0.69	3	-
GCA_018674025.1	s__SGZJ01 sp018674025	86.5744	265	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182835.1	s__SGZJ01 sp905182835	80.2826	262	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512065.1	s__GCA-2700405 sp902512065	76.4518	61	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	76.1473	67	383	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_018657955.1	s__GCA-2700405 sp018657955	76.1278	67	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	99.95	99.87	0.95	0.89	9	-
GCF_014297365.1	s__Winogradskyella echinorum	76.0669	52	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003443635.1	s__AU392 sp003443635	75.9176	60	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:49:50,924] [INFO] GTDB search result was written to OceanDNA-b6302/result_gtdb.tsv
[2023-03-15 07:49:50,927] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:49:50,930] [INFO] DFAST_QC result json was written to OceanDNA-b6302/dqc_result.json
[2023-03-15 07:49:50,930] [INFO] DFAST_QC completed!
[2023-03-15 07:49:50,930] [INFO] Total running time: 0h0m51s