[2023-03-15 05:58:27,560] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:58:27,569] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:58:27,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgece5fb58-6b68-4514-abb7-5982b7343687/dqc_reference
[2023-03-15 05:58:28,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:58:28,709] [INFO] Task started: Prodigal
[2023-03-15 05:58:28,709] [INFO] Running command: cat /var/lib/cwl/stg025c8783-b347-4fb0-9c71-84d178e387ba/OceanDNA-a4715.fa | prodigal -d OceanDNA-a4715/cds.fna -a OceanDNA-a4715/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:58:36,425] [INFO] Task succeeded: Prodigal
[2023-03-15 05:58:36,425] [INFO] Task started: HMMsearch
[2023-03-15 05:58:36,425] [INFO] Running command: hmmsearch --tblout OceanDNA-a4715/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgece5fb58-6b68-4514-abb7-5982b7343687/dqc_reference/reference_markers.hmm OceanDNA-a4715/protein.faa > /dev/null
[2023-03-15 05:58:36,604] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:58:36,605] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg025c8783-b347-4fb0-9c71-84d178e387ba/OceanDNA-a4715.fa]
[2023-03-15 05:58:36,695] [INFO] Query marker FASTA was written to OceanDNA-a4715/markers.fasta
[2023-03-15 05:58:36,696] [INFO] Task started: Blastn
[2023-03-15 05:58:36,697] [INFO] Running command: blastn -query OceanDNA-a4715/markers.fasta -db /var/lib/cwl/stgece5fb58-6b68-4514-abb7-5982b7343687/dqc_reference/reference_markers.fasta -out OceanDNA-a4715/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:58:37,180] [INFO] Task succeeded: Blastn
[2023-03-15 05:58:37,208] [INFO] Selected 4 target genomes.
[2023-03-15 05:58:37,209] [INFO] Target genome list was writen to OceanDNA-a4715/target_genomes.txt
[2023-03-15 05:58:37,211] [INFO] Task started: fastANI
[2023-03-15 05:58:37,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg025c8783-b347-4fb0-9c71-84d178e387ba/OceanDNA-a4715.fa --refList OceanDNA-a4715/target_genomes.txt --output OceanDNA-a4715/fastani_result.tsv --threads 1
[2023-03-15 05:58:39,310] [INFO] Task succeeded: fastANI
[2023-03-15 05:58:39,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgece5fb58-6b68-4514-abb7-5982b7343687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:58:39,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgece5fb58-6b68-4514-abb7-5982b7343687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:58:39,311] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:58:39,311] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:58:39,311] [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 05:58:39,322] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4715/tc_result.tsv
[2023-03-15 05:58:39,340] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:58:39,340] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:58:39,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgece5fb58-6b68-4514-abb7-5982b7343687/dqc_reference/checkm_data
[2023-03-15 05:58:39,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:58:39,368] [INFO] Task started: CheckM
[2023-03-15 05:58:39,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4715/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4715/checkm_input OceanDNA-a4715/checkm_result
[2023-03-15 05:59:03,898] [INFO] Task succeeded: CheckM
[2023-03-15 05:59:03,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:59:04,106] [INFO] ===== Completeness check finished =====
[2023-03-15 05:59:04,107] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:59:04,107] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4715/markers.fasta)
[2023-03-15 05:59:04,108] [INFO] Task started: Blastn
[2023-03-15 05:59:04,108] [INFO] Running command: blastn -query OceanDNA-a4715/markers.fasta -db /var/lib/cwl/stgece5fb58-6b68-4514-abb7-5982b7343687/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4715/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:59:04,699] [INFO] Task succeeded: Blastn
[2023-03-15 05:59:04,732] [INFO] Selected 6 target genomes.
[2023-03-15 05:59:04,732] [INFO] Target genome list was writen to OceanDNA-a4715/target_genomes_gtdb.txt
[2023-03-15 05:59:04,740] [INFO] Task started: fastANI
[2023-03-15 05:59:04,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg025c8783-b347-4fb0-9c71-84d178e387ba/OceanDNA-a4715.fa --refList OceanDNA-a4715/target_genomes_gtdb.txt --output OceanDNA-a4715/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:59:06,294] [INFO] Task succeeded: fastANI
[2023-03-15 05:59:06,298] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:59:06,298] [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_002718995.2	s__MGIIb-O5 sp002718995	99.866	422	428	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.42	98.33	0.97	0.95	5	conclusive
GCA_002498925.1	s__MGIIb-O5 sp002498925	88.226	331	428	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.31	97.86	0.85	0.82	9	-
GCA_002504435.1	s__MGIIb-O5 sp002504435	80.8699	274	428	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.62	99.62	0.76	0.76	2	-
GCA_002497985.1	s__MGIIb-O5 sp002497985	78.6927	151	428	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	95.38	95.38	0.60	0.60	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:59:06,312] [INFO] GTDB search result was written to OceanDNA-a4715/result_gtdb.tsv
[2023-03-15 05:59:06,329] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:59:06,344] [INFO] DFAST_QC result json was written to OceanDNA-a4715/dqc_result.json
[2023-03-15 05:59:06,344] [INFO] DFAST_QC completed!
[2023-03-15 05:59:06,344] [INFO] Total running time: 0h0m39s