[2023-03-17 10:48:45,648] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,648] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg0af06105-775b-461a-9171-4673a11b2da3/dqc_reference
[2023-03-17 10:48:46,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,781] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,781] [INFO] Running command: cat /var/lib/cwl/stgb7a925a8-2e09-4c32-a3d0-5496afa70f3d/OceanDNA-a2638.fa | prodigal -d OceanDNA-a2638/cds.fna -a OceanDNA-a2638/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:54,910] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:54,910] [INFO] Task started: HMMsearch
[2023-03-17 10:48:54,910] [INFO] Running command: hmmsearch --tblout OceanDNA-a2638/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0af06105-775b-461a-9171-4673a11b2da3/dqc_reference/reference_markers.hmm OceanDNA-a2638/protein.faa > /dev/null
[2023-03-17 10:48:55,063] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:55,063] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb7a925a8-2e09-4c32-a3d0-5496afa70f3d/OceanDNA-a2638.fa]
[2023-03-17 10:48:55,077] [INFO] Query marker FASTA was written to OceanDNA-a2638/markers.fasta
[2023-03-17 10:48:55,077] [INFO] Task started: Blastn
[2023-03-17 10:48:55,077] [INFO] Running command: blastn -query OceanDNA-a2638/markers.fasta -db /var/lib/cwl/stg0af06105-775b-461a-9171-4673a11b2da3/dqc_reference/reference_markers.fasta -out OceanDNA-a2638/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:55,516] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:55,517] [INFO] Selected 1 target genomes.
[2023-03-17 10:48:55,518] [INFO] Target genome list was writen to OceanDNA-a2638/target_genomes.txt
[2023-03-17 10:48:55,519] [INFO] Task started: fastANI
[2023-03-17 10:48:55,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7a925a8-2e09-4c32-a3d0-5496afa70f3d/OceanDNA-a2638.fa --refList OceanDNA-a2638/target_genomes.txt --output OceanDNA-a2638/fastani_result.tsv --threads 1
[2023-03-17 10:48:55,837] [INFO] Task succeeded: fastANI
[2023-03-17 10:48:55,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0af06105-775b-461a-9171-4673a11b2da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:48:55,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0af06105-775b-461a-9171-4673a11b2da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:48:55,837] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:48:55,837] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:48:55,837] [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
--------------------------------------------------------------------------------
[2023-03-17 10:48:55,838] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2638/tc_result.tsv
[2023-03-17 10:48:55,838] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:48:55,838] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:48:55,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0af06105-775b-461a-9171-4673a11b2da3/dqc_reference/checkm_data
[2023-03-17 10:48:55,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:48:55,846] [INFO] Task started: CheckM
[2023-03-17 10:48:55,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2638/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2638/checkm_input OceanDNA-a2638/checkm_result
[2023-03-17 10:49:21,881] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:21,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.27%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:21,883] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:21,883] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:21,884] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2638/markers.fasta)
[2023-03-17 10:49:21,884] [INFO] Task started: Blastn
[2023-03-17 10:49:21,884] [INFO] Running command: blastn -query OceanDNA-a2638/markers.fasta -db /var/lib/cwl/stg0af06105-775b-461a-9171-4673a11b2da3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2638/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:22,362] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:22,363] [INFO] Selected 5 target genomes.
[2023-03-17 10:49:22,363] [INFO] Target genome list was writen to OceanDNA-a2638/target_genomes_gtdb.txt
[2023-03-17 10:49:22,440] [INFO] Task started: fastANI
[2023-03-17 10:49:22,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7a925a8-2e09-4c32-a3d0-5496afa70f3d/OceanDNA-a2638.fa --refList OceanDNA-a2638/target_genomes_gtdb.txt --output OceanDNA-a2638/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:24,543] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:24,548] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:49:24,548] [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_013329925.1	s__MGIIa-L1 sp8734u	99.2027	372	480	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCA_002688825.1	s__MGIIa-L1 sp002688825	88.5036	277	480	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726395.1	s__MGIIa-L1 sp002726395	86.2451	373	480	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.39	99.39	0.85	0.85	2	-
GCA_009887195.1	s__MGIIa-L1 sp009887195	85.4182	378	480	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.91	98.88	0.90	0.86	3	-
GCA_018659375.1	s__MGIIa-L1 sp018659375	84.4283	413	480	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:24,548] [INFO] GTDB search result was written to OceanDNA-a2638/result_gtdb.tsv
[2023-03-17 10:49:24,549] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:24,549] [INFO] DFAST_QC result json was written to OceanDNA-a2638/dqc_result.json
[2023-03-17 10:49:24,549] [INFO] DFAST_QC completed!
[2023-03-17 10:49:24,550] [INFO] Total running time: 0h0m39s