[2023-03-14 13:05:43,392] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:05:43,392] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:05:43,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg90eecc55-4458-4a70-aeb1-cfcd86ea2466/dqc_reference
[2023-03-14 13:05:44,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:05:44,550] [INFO] Task started: Prodigal
[2023-03-14 13:05:44,551] [INFO] Running command: cat /var/lib/cwl/stg3147670d-ab1a-4582-9e99-52d31849342b/OceanDNA-b8722.fa | prodigal -d OceanDNA-b8722/cds.fna -a OceanDNA-b8722/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:05:49,545] [INFO] Task succeeded: Prodigal
[2023-03-14 13:05:49,545] [INFO] Task started: HMMsearch
[2023-03-14 13:05:49,545] [INFO] Running command: hmmsearch --tblout OceanDNA-b8722/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90eecc55-4458-4a70-aeb1-cfcd86ea2466/dqc_reference/reference_markers.hmm OceanDNA-b8722/protein.faa > /dev/null
[2023-03-14 13:05:49,702] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:05:49,703] [INFO] Found 6/6 markers.
[2023-03-14 13:05:49,711] [INFO] Query marker FASTA was written to OceanDNA-b8722/markers.fasta
[2023-03-14 13:05:49,711] [INFO] Task started: Blastn
[2023-03-14 13:05:49,711] [INFO] Running command: blastn -query OceanDNA-b8722/markers.fasta -db /var/lib/cwl/stg90eecc55-4458-4a70-aeb1-cfcd86ea2466/dqc_reference/reference_markers.fasta -out OceanDNA-b8722/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:05:50,292] [INFO] Task succeeded: Blastn
[2023-03-14 13:05:50,293] [INFO] Selected 27 target genomes.
[2023-03-14 13:05:50,293] [INFO] Target genome list was writen to OceanDNA-b8722/target_genomes.txt
[2023-03-14 13:05:50,311] [INFO] Task started: fastANI
[2023-03-14 13:05:50,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg3147670d-ab1a-4582-9e99-52d31849342b/OceanDNA-b8722.fa --refList OceanDNA-b8722/target_genomes.txt --output OceanDNA-b8722/fastani_result.tsv --threads 1
[2023-03-14 13:06:11,590] [INFO] Task succeeded: fastANI
[2023-03-14 13:06:11,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90eecc55-4458-4a70-aeb1-cfcd86ea2466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:06:11,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90eecc55-4458-4a70-aeb1-cfcd86ea2466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:06:11,591] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:06:11,591] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:06:11,591] [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
--------------------------------------------------------------------------------
[2023-03-14 13:06:11,591] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8722/tc_result.tsv
[2023-03-14 13:06:11,591] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:06:11,591] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:06:11,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90eecc55-4458-4a70-aeb1-cfcd86ea2466/dqc_reference/checkm_data
[2023-03-14 13:06:11,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:06:11,599] [INFO] Task started: CheckM
[2023-03-14 13:06:11,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8722/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8722/checkm_input OceanDNA-b8722/checkm_result
[2023-03-14 13:06:33,904] [INFO] Task succeeded: CheckM
[2023-03-14 13:06:33,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:06:33,906] [INFO] ===== Completeness check finished =====
[2023-03-14 13:06:33,906] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:06:33,906] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8722/markers.fasta)
[2023-03-14 13:06:33,908] [INFO] Task started: Blastn
[2023-03-14 13:06:33,908] [INFO] Running command: blastn -query OceanDNA-b8722/markers.fasta -db /var/lib/cwl/stg90eecc55-4458-4a70-aeb1-cfcd86ea2466/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8722/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:06:34,966] [INFO] Task succeeded: Blastn
[2023-03-14 13:06:34,966] [INFO] Selected 14 target genomes.
[2023-03-14 13:06:34,966] [INFO] Target genome list was writen to OceanDNA-b8722/target_genomes_gtdb.txt
[2023-03-14 13:06:34,982] [INFO] Task started: fastANI
[2023-03-14 13:06:34,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg3147670d-ab1a-4582-9e99-52d31849342b/OceanDNA-b8722.fa --refList OceanDNA-b8722/target_genomes_gtdb.txt --output OceanDNA-b8722/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:06:38,811] [INFO] Task succeeded: fastANI
[2023-03-14 13:06:38,819] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:06:38,819] [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_008081325.1	s__MED-G13 sp008081325	97.5135	168	235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902518355.1	s__MED-G13 sp902518355	82.2113	191	235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_002702745.1	s__MED-G13 sp002702745	82.1862	172	235	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	81.8917	164	235	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_002691265.1	s__MED-G13 sp002691265	81.8148	197	235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.61	95.49	0.82	0.79	4	-
GCA_902604715.1	s__MED-G13 sp902604715	79.7147	129	235	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_902626365.1	s__MED-G13 sp902626365	79.6815	153	235	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_902519075.1	s__MED-G13 sp902519075	79.4517	137	235	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_902517895.1	s__MED-G13 sp902517895	79.2827	126	235	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_902608795.1	s__MED-G13 sp902608795	79.2049	120	235	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	78.8916	145	235	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_002697255.1	s__MED-G13 sp002697255	77.8656	131	235	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:06:38,819] [INFO] GTDB search result was written to OceanDNA-b8722/result_gtdb.tsv
[2023-03-14 13:06:38,819] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:06:38,820] [INFO] DFAST_QC result json was written to OceanDNA-b8722/dqc_result.json
[2023-03-14 13:06:38,821] [INFO] DFAST_QC completed!
[2023-03-14 13:06:38,821] [INFO] Total running time: 0h0m55s