[2023-03-16 23:05:03,912] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,912] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,913] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4678f79-2cd2-4b52-8407-c3763d5d3816/dqc_reference
[2023-03-16 23:05:05,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stg2cedf85c-7edc-4ef2-a954-35ab8fe964dd/OceanDNA-b11932.fa | prodigal -d OceanDNA-b11932/cds.fna -a OceanDNA-b11932/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:27,954] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:27,955] [INFO] Task started: HMMsearch
[2023-03-16 23:05:27,955] [INFO] Running command: hmmsearch --tblout OceanDNA-b11932/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4678f79-2cd2-4b52-8407-c3763d5d3816/dqc_reference/reference_markers.hmm OceanDNA-b11932/protein.faa > /dev/null
[2023-03-16 23:05:28,156] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:28,157] [INFO] Found 6/6 markers.
[2023-03-16 23:05:28,172] [INFO] Query marker FASTA was written to OceanDNA-b11932/markers.fasta
[2023-03-16 23:05:28,172] [INFO] Task started: Blastn
[2023-03-16 23:05:28,172] [INFO] Running command: blastn -query OceanDNA-b11932/markers.fasta -db /var/lib/cwl/stgd4678f79-2cd2-4b52-8407-c3763d5d3816/dqc_reference/reference_markers.fasta -out OceanDNA-b11932/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:28,718] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:28,719] [INFO] Selected 25 target genomes.
[2023-03-16 23:05:28,719] [INFO] Target genome list was writen to OceanDNA-b11932/target_genomes.txt
[2023-03-16 23:05:28,731] [INFO] Task started: fastANI
[2023-03-16 23:05:28,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cedf85c-7edc-4ef2-a954-35ab8fe964dd/OceanDNA-b11932.fa --refList OceanDNA-b11932/target_genomes.txt --output OceanDNA-b11932/fastani_result.tsv --threads 1
[2023-03-16 23:05:46,692] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:46,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4678f79-2cd2-4b52-8407-c3763d5d3816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:46,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4678f79-2cd2-4b52-8407-c3763d5d3816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:46,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:46,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:05:46,693] [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
--------------------------------------------------------------------------------
[2023-03-16 23:05:46,693] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11932/tc_result.tsv
[2023-03-16 23:05:46,694] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:46,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:46,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4678f79-2cd2-4b52-8407-c3763d5d3816/dqc_reference/checkm_data
[2023-03-16 23:05:46,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:46,700] [INFO] Task started: CheckM
[2023-03-16 23:05:46,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11932/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11932/checkm_input OceanDNA-b11932/checkm_result
[2023-03-16 23:06:58,403] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:58,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:58,405] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:58,405] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:58,406] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11932/markers.fasta)
[2023-03-16 23:06:58,406] [INFO] Task started: Blastn
[2023-03-16 23:06:58,406] [INFO] Running command: blastn -query OceanDNA-b11932/markers.fasta -db /var/lib/cwl/stgd4678f79-2cd2-4b52-8407-c3763d5d3816/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11932/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:59,141] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:59,142] [INFO] Selected 16 target genomes.
[2023-03-16 23:06:59,142] [INFO] Target genome list was writen to OceanDNA-b11932/target_genomes_gtdb.txt
[2023-03-16 23:06:59,895] [INFO] Task started: fastANI
[2023-03-16 23:06:59,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cedf85c-7edc-4ef2-a954-35ab8fe964dd/OceanDNA-b11932.fa --refList OceanDNA-b11932/target_genomes_gtdb.txt --output OceanDNA-b11932/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:07:05,556] [INFO] Task succeeded: fastANI
[2023-03-16 23:07:05,562] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:07:05,562] [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_002469765.1	s__UBA11663 sp002469765	98.4425	490	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002729115.1	s__UBA11663 sp002729115	85.1065	395	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	96.51	95.05	0.71	0.69	4	-
GCA_002863145.1	s__UBA11663 sp002863145	78.5135	247	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
GCA_002683345.1	s__UBA11663 sp002683345	78.1244	222	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524845.1	s__UBA11663 sp011524845	78.0528	197	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002313415.1	s__UBA11663 sp002313415	77.1303	119	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	99.13	99.10	0.82	0.81	3	-
GCA_002172485.2	s__UBA8752 sp002172485	76.0476	53	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863125.1	s__UA16 sp002863125	76.0347	81	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	97.01	95.79	0.91	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-16 23:07:05,562] [INFO] GTDB search result was written to OceanDNA-b11932/result_gtdb.tsv
[2023-03-16 23:07:05,562] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:07:05,563] [INFO] DFAST_QC result json was written to OceanDNA-b11932/dqc_result.json
[2023-03-16 23:07:05,563] [INFO] DFAST_QC completed!
[2023-03-16 23:07:05,563] [INFO] Total running time: 0h2m2s