[2023-03-15 16:00:11,278] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:00:11,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:00:11,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg56944864-4ce3-496b-ba86-d47196be8d4f/dqc_reference
[2023-03-15 16:00:14,600] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:00:14,601] [INFO] Task started: Prodigal
[2023-03-15 16:00:14,601] [INFO] Running command: cat /var/lib/cwl/stg534911f0-9dd5-48bd-9cb0-212b796458a3/OceanDNA-b3862.fa | prodigal -d OceanDNA-b3862/cds.fna -a OceanDNA-b3862/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:00:22,416] [INFO] Task succeeded: Prodigal
[2023-03-15 16:00:22,417] [INFO] Task started: HMMsearch
[2023-03-15 16:00:22,417] [INFO] Running command: hmmsearch --tblout OceanDNA-b3862/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56944864-4ce3-496b-ba86-d47196be8d4f/dqc_reference/reference_markers.hmm OceanDNA-b3862/protein.faa > /dev/null
[2023-03-15 16:00:22,566] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:00:22,567] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg534911f0-9dd5-48bd-9cb0-212b796458a3/OceanDNA-b3862.fa]
[2023-03-15 16:00:22,579] [INFO] Query marker FASTA was written to OceanDNA-b3862/markers.fasta
[2023-03-15 16:00:22,581] [INFO] Task started: Blastn
[2023-03-15 16:00:22,581] [INFO] Running command: blastn -query OceanDNA-b3862/markers.fasta -db /var/lib/cwl/stg56944864-4ce3-496b-ba86-d47196be8d4f/dqc_reference/reference_markers.fasta -out OceanDNA-b3862/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:00:23,103] [INFO] Task succeeded: Blastn
[2023-03-15 16:00:23,103] [INFO] Selected 21 target genomes.
[2023-03-15 16:00:23,104] [INFO] Target genome list was writen to OceanDNA-b3862/target_genomes.txt
[2023-03-15 16:00:23,117] [INFO] Task started: fastANI
[2023-03-15 16:00:23,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg534911f0-9dd5-48bd-9cb0-212b796458a3/OceanDNA-b3862.fa --refList OceanDNA-b3862/target_genomes.txt --output OceanDNA-b3862/fastani_result.tsv --threads 1
[2023-03-15 16:00:34,036] [INFO] Task succeeded: fastANI
[2023-03-15 16:00:34,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56944864-4ce3-496b-ba86-d47196be8d4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:00:34,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56944864-4ce3-496b-ba86-d47196be8d4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:00:34,037] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:00:34,037] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:00:34,037] [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
--------------------------------------------------------------------------------
[2023-03-15 16:00:34,037] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3862/tc_result.tsv
[2023-03-15 16:00:34,037] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:00:34,037] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:00:34,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56944864-4ce3-496b-ba86-d47196be8d4f/dqc_reference/checkm_data
[2023-03-15 16:00:34,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:00:34,097] [INFO] Task started: CheckM
[2023-03-15 16:00:34,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3862/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3862/checkm_input OceanDNA-b3862/checkm_result
[2023-03-15 16:01:02,835] [INFO] Task succeeded: CheckM
[2023-03-15 16:01:02,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.29%
Contamintation: 2.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 16:01:02,838] [INFO] ===== Completeness check finished =====
[2023-03-15 16:01:02,838] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:01:02,838] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3862/markers.fasta)
[2023-03-15 16:01:02,839] [INFO] Task started: Blastn
[2023-03-15 16:01:02,839] [INFO] Running command: blastn -query OceanDNA-b3862/markers.fasta -db /var/lib/cwl/stg56944864-4ce3-496b-ba86-d47196be8d4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3862/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:01:03,843] [INFO] Task succeeded: Blastn
[2023-03-15 16:01:03,844] [INFO] Selected 18 target genomes.
[2023-03-15 16:01:03,844] [INFO] Target genome list was writen to OceanDNA-b3862/target_genomes_gtdb.txt
[2023-03-15 16:01:03,863] [INFO] Task started: fastANI
[2023-03-15 16:01:03,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg534911f0-9dd5-48bd-9cb0-212b796458a3/OceanDNA-b3862.fa --refList OceanDNA-b3862/target_genomes_gtdb.txt --output OceanDNA-b3862/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:01:13,481] [INFO] Task succeeded: fastANI
[2023-03-15 16:01:13,484] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:01:13,484] [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_002862745.1	s__UBA8649 sp002862745	95.2213	244	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA8649;g__UBA8649	95.0	98.42	97.54	0.94	0.94	3	conclusive
GCA_002708985.1	s__UBA8649 sp002708985	86.5989	226	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA8649;g__UBA8649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447535.1	s__UBA8649 sp003447535	86.1618	195	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA8649;g__UBA8649	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:01:13,484] [INFO] GTDB search result was written to OceanDNA-b3862/result_gtdb.tsv
[2023-03-15 16:01:13,485] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:01:13,485] [INFO] DFAST_QC result json was written to OceanDNA-b3862/dqc_result.json
[2023-03-15 16:01:13,485] [INFO] DFAST_QC completed!
[2023-03-15 16:01:13,486] [INFO] Total running time: 0h1m2s