[2023-03-18 07:29:30,341] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,341] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c62357e-f1ec-4679-9c54-27f54eb54fec/dqc_reference
[2023-03-18 07:29:31,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,938] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,938] [INFO] Running command: cat /var/lib/cwl/stge6fc8bfb-9f2e-47ba-bbf1-ce02858d1db1/OceanDNA-a4095.fa | prodigal -d OceanDNA-a4095/cds.fna -a OceanDNA-a4095/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:38,408] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:38,409] [INFO] Task started: HMMsearch
[2023-03-18 07:29:38,409] [INFO] Running command: hmmsearch --tblout OceanDNA-a4095/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c62357e-f1ec-4679-9c54-27f54eb54fec/dqc_reference/reference_markers.hmm OceanDNA-a4095/protein.faa > /dev/null
[2023-03-18 07:29:38,562] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:38,563] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge6fc8bfb-9f2e-47ba-bbf1-ce02858d1db1/OceanDNA-a4095.fa]
[2023-03-18 07:29:38,571] [INFO] Query marker FASTA was written to OceanDNA-a4095/markers.fasta
[2023-03-18 07:29:38,571] [INFO] Task started: Blastn
[2023-03-18 07:29:38,571] [INFO] Running command: blastn -query OceanDNA-a4095/markers.fasta -db /var/lib/cwl/stg5c62357e-f1ec-4679-9c54-27f54eb54fec/dqc_reference/reference_markers.fasta -out OceanDNA-a4095/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:39,016] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:39,017] [INFO] Selected 5 target genomes.
[2023-03-18 07:29:39,017] [INFO] Target genome list was writen to OceanDNA-a4095/target_genomes.txt
[2023-03-18 07:29:39,021] [INFO] Task started: fastANI
[2023-03-18 07:29:39,021] [INFO] Running command: fastANI --query /var/lib/cwl/stge6fc8bfb-9f2e-47ba-bbf1-ce02858d1db1/OceanDNA-a4095.fa --refList OceanDNA-a4095/target_genomes.txt --output OceanDNA-a4095/fastani_result.tsv --threads 1
[2023-03-18 07:29:41,966] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:41,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c62357e-f1ec-4679-9c54-27f54eb54fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:41,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c62357e-f1ec-4679-9c54-27f54eb54fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:41,967] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:41,967] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:41,967] [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 07:29:41,967] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4095/tc_result.tsv
[2023-03-18 07:29:41,967] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:41,967] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:41,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c62357e-f1ec-4679-9c54-27f54eb54fec/dqc_reference/checkm_data
[2023-03-18 07:29:41,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:41,972] [INFO] Task started: CheckM
[2023-03-18 07:29:41,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4095/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4095/checkm_input OceanDNA-a4095/checkm_result
[2023-03-18 07:30:03,605] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:03,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:03,607] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:03,607] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:03,607] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4095/markers.fasta)
[2023-03-18 07:30:03,607] [INFO] Task started: Blastn
[2023-03-18 07:30:03,607] [INFO] Running command: blastn -query OceanDNA-a4095/markers.fasta -db /var/lib/cwl/stg5c62357e-f1ec-4679-9c54-27f54eb54fec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4095/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:04,129] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:04,130] [INFO] Selected 6 target genomes.
[2023-03-18 07:30:04,130] [INFO] Target genome list was writen to OceanDNA-a4095/target_genomes_gtdb.txt
[2023-03-18 07:30:04,309] [INFO] Task started: fastANI
[2023-03-18 07:30:04,309] [INFO] Running command: fastANI --query /var/lib/cwl/stge6fc8bfb-9f2e-47ba-bbf1-ce02858d1db1/OceanDNA-a4095.fa --refList OceanDNA-a4095/target_genomes_gtdb.txt --output OceanDNA-a4095/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:05,796] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:05,799] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:05,799] [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_002725315.1	s__MGIIb-O3 sp002725315	77.4861	81	363	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.12	98.81	0.90	0.86	5	-
GCA_001628485.1	s__MGIIb-O3 sp001628485	76.9441	69	363	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.15	97.12	0.88	0.79	10	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:05,799] [INFO] GTDB search result was written to OceanDNA-a4095/result_gtdb.tsv
[2023-03-18 07:30:05,799] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:05,800] [INFO] DFAST_QC result json was written to OceanDNA-a4095/dqc_result.json
[2023-03-18 07:30:05,800] [INFO] DFAST_QC completed!
[2023-03-18 07:30:05,800] [INFO] Total running time: 0h0m35s