[2023-03-17 16:38:19,311] [INFO] DFAST_QC pipeline started.
[2023-03-17 16:38:19,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 16:38:19,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c968d8d-1c94-4497-9ec1-a2bdf884903d/dqc_reference
[2023-03-17 16:38:20,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 16:38:20,853] [INFO] Task started: Prodigal
[2023-03-17 16:38:20,853] [INFO] Running command: cat /var/lib/cwl/stg30f8cd02-6768-48a3-82a2-195a16020bf3/OceanDNA-a2183.fa | prodigal -d OceanDNA-a2183/cds.fna -a OceanDNA-a2183/protein.faa -g 11 -q > /dev/null
[2023-03-17 16:38:36,553] [INFO] Task succeeded: Prodigal
[2023-03-17 16:38:36,553] [INFO] Task started: HMMsearch
[2023-03-17 16:38:36,553] [INFO] Running command: hmmsearch --tblout OceanDNA-a2183/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c968d8d-1c94-4497-9ec1-a2bdf884903d/dqc_reference/reference_markers.hmm OceanDNA-a2183/protein.faa > /dev/null
[2023-03-17 16:38:36,958] [INFO] Task succeeded: HMMsearch
[2023-03-17 16:38:36,959] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg30f8cd02-6768-48a3-82a2-195a16020bf3/OceanDNA-a2183.fa]
[2023-03-17 16:38:36,973] [INFO] Query marker FASTA was written to OceanDNA-a2183/markers.fasta
[2023-03-17 16:38:36,973] [INFO] Task started: Blastn
[2023-03-17 16:38:36,973] [INFO] Running command: blastn -query OceanDNA-a2183/markers.fasta -db /var/lib/cwl/stg0c968d8d-1c94-4497-9ec1-a2bdf884903d/dqc_reference/reference_markers.fasta -out OceanDNA-a2183/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:38:37,987] [INFO] Task succeeded: Blastn
[2023-03-17 16:38:37,988] [INFO] Selected 5 target genomes.
[2023-03-17 16:38:37,988] [INFO] Target genome list was writen to OceanDNA-a2183/target_genomes.txt
[2023-03-17 16:38:37,991] [INFO] Task started: fastANI
[2023-03-17 16:38:37,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f8cd02-6768-48a3-82a2-195a16020bf3/OceanDNA-a2183.fa --refList OceanDNA-a2183/target_genomes.txt --output OceanDNA-a2183/fastani_result.tsv --threads 1
[2023-03-17 16:38:42,709] [INFO] Task succeeded: fastANI
[2023-03-17 16:38:42,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c968d8d-1c94-4497-9ec1-a2bdf884903d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 16:38:42,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c968d8d-1c94-4497-9ec1-a2bdf884903d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 16:38:42,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 16:38:42,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 16:38:42,710] [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 16:38:42,710] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2183/tc_result.tsv
[2023-03-17 16:38:42,710] [INFO] ===== Taxonomy check completed =====
[2023-03-17 16:38:42,711] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 16:38:42,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c968d8d-1c94-4497-9ec1-a2bdf884903d/dqc_reference/checkm_data
[2023-03-17 16:38:42,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 16:38:42,717] [INFO] Task started: CheckM
[2023-03-17 16:38:42,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2183/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2183/checkm_input OceanDNA-a2183/checkm_result
[2023-03-17 16:39:21,148] [INFO] Task succeeded: CheckM
[2023-03-17 16:39:21,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 16:39:21,150] [INFO] ===== Completeness check finished =====
[2023-03-17 16:39:21,150] [INFO] ===== Start GTDB Search =====
[2023-03-17 16:39:21,150] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2183/markers.fasta)
[2023-03-17 16:39:21,151] [INFO] Task started: Blastn
[2023-03-17 16:39:21,151] [INFO] Running command: blastn -query OceanDNA-a2183/markers.fasta -db /var/lib/cwl/stg0c968d8d-1c94-4497-9ec1-a2bdf884903d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2183/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:39:22,394] [INFO] Task succeeded: Blastn
[2023-03-17 16:39:22,395] [INFO] Selected 10 target genomes.
[2023-03-17 16:39:22,395] [INFO] Target genome list was writen to OceanDNA-a2183/target_genomes_gtdb.txt
[2023-03-17 16:39:22,887] [INFO] Task started: fastANI
[2023-03-17 16:39:22,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f8cd02-6768-48a3-82a2-195a16020bf3/OceanDNA-a2183.fa --refList OceanDNA-a2183/target_genomes_gtdb.txt --output OceanDNA-a2183/fastani_result_gtdb.tsv --threads 1
[2023-03-17 16:39:26,520] [INFO] Task succeeded: fastANI
[2023-03-17 16:39:26,526] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 16:39:26,526] [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_011526375.1	s__MGIIa-L1 sp011526375	81.6017	422	600	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_013329295.1	s__MGIIa-L1 sp9596u	78.7792	213	600	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
GCA_002496955.1	s__MGIIa-L1 sp002496955	78.0912	144	600	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.33	98.29	0.73	0.72	3	-
GCA_009887195.1	s__MGIIa-L1 sp009887195	77.7415	163	600	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_002727485.1	s__MGIIa-L1 sp002727485	77.5325	69	600	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_002505355.1	s__MGIIa-L1 sp002505355	77.3007	147	600	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	76.9613	132	600	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_002172355.2	s__MGIIa-L1 sp002172355	76.7994	79	600	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.37	98.74	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-17 16:39:26,526] [INFO] GTDB search result was written to OceanDNA-a2183/result_gtdb.tsv
[2023-03-17 16:39:26,526] [INFO] ===== GTDB Search completed =====
[2023-03-17 16:39:26,527] [INFO] DFAST_QC result json was written to OceanDNA-a2183/dqc_result.json
[2023-03-17 16:39:26,527] [INFO] DFAST_QC completed!
[2023-03-17 16:39:26,527] [INFO] Total running time: 0h1m7s