[2023-03-15 11:51:17,346] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,346] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,346] [INFO] DQC Reference Directory: /var/lib/cwl/stga1ae9122-f7c2-4183-8821-8021656d6bc8/dqc_reference
[2023-03-15 11:51:18,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,950] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,950] [INFO] Running command: cat /var/lib/cwl/stgc098500c-1c48-4f98-b671-cc5b0bd86a95/OceanDNA-a3147.fa | prodigal -d OceanDNA-a3147/cds.fna -a OceanDNA-a3147/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:28,012] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:28,012] [INFO] Task started: HMMsearch
[2023-03-15 11:51:28,012] [INFO] Running command: hmmsearch --tblout OceanDNA-a3147/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1ae9122-f7c2-4183-8821-8021656d6bc8/dqc_reference/reference_markers.hmm OceanDNA-a3147/protein.faa > /dev/null
[2023-03-15 11:51:28,163] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:28,163] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc098500c-1c48-4f98-b671-cc5b0bd86a95/OceanDNA-a3147.fa]
[2023-03-15 11:51:28,174] [INFO] Query marker FASTA was written to OceanDNA-a3147/markers.fasta
[2023-03-15 11:51:28,175] [INFO] Task started: Blastn
[2023-03-15 11:51:28,175] [INFO] Running command: blastn -query OceanDNA-a3147/markers.fasta -db /var/lib/cwl/stga1ae9122-f7c2-4183-8821-8021656d6bc8/dqc_reference/reference_markers.fasta -out OceanDNA-a3147/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:28,626] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:28,627] [INFO] Selected 5 target genomes.
[2023-03-15 11:51:28,627] [INFO] Target genome list was writen to OceanDNA-a3147/target_genomes.txt
[2023-03-15 11:51:28,631] [INFO] Task started: fastANI
[2023-03-15 11:51:28,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgc098500c-1c48-4f98-b671-cc5b0bd86a95/OceanDNA-a3147.fa --refList OceanDNA-a3147/target_genomes.txt --output OceanDNA-a3147/fastani_result.tsv --threads 1
[2023-03-15 11:51:31,274] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:31,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1ae9122-f7c2-4183-8821-8021656d6bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:31,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1ae9122-f7c2-4183-8821-8021656d6bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:31,275] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:31,275] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:51:31,275] [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 11:51:31,275] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3147/tc_result.tsv
[2023-03-15 11:51:31,276] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:31,276] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:31,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1ae9122-f7c2-4183-8821-8021656d6bc8/dqc_reference/checkm_data
[2023-03-15 11:51:31,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:31,325] [INFO] Task started: CheckM
[2023-03-15 11:51:31,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3147/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3147/checkm_input OceanDNA-a3147/checkm_result
[2023-03-15 11:52:01,953] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:01,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:01,955] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:01,955] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:01,956] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3147/markers.fasta)
[2023-03-15 11:52:01,956] [INFO] Task started: Blastn
[2023-03-15 11:52:01,957] [INFO] Running command: blastn -query OceanDNA-a3147/markers.fasta -db /var/lib/cwl/stga1ae9122-f7c2-4183-8821-8021656d6bc8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3147/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:02,405] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:02,406] [INFO] Selected 8 target genomes.
[2023-03-15 11:52:02,406] [INFO] Target genome list was writen to OceanDNA-a3147/target_genomes_gtdb.txt
[2023-03-15 11:52:02,439] [INFO] Task started: fastANI
[2023-03-15 11:52:02,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgc098500c-1c48-4f98-b671-cc5b0bd86a95/OceanDNA-a3147.fa --refList OceanDNA-a3147/target_genomes_gtdb.txt --output OceanDNA-a3147/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:05,179] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:05,184] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:52:05,184] [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_013330155.1	s__Poseidonia sp8339u	98.4929	305	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.08	98.16	0.89	0.82	3	conclusive
GCA_002704515.1	s__Poseidonia sp002704515	91.0052	326	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714305.1	s__Poseidonia sp002714305	86.4303	336	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_002502295.1	s__Poseidonia sp002502295	80.7902	315	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497765.1	s__Poseidonia sp002497765	78.7161	204	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.70	99.65	0.88	0.86	3	-
GCA_002689105.1	s__Poseidonia sp002689105	78.4164	198	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_016779705.1	s__Poseidonia sp016779705	77.4609	103	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602485.1	s__Poseidonia sp003602485	77.0057	82	427	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:05,185] [INFO] GTDB search result was written to OceanDNA-a3147/result_gtdb.tsv
[2023-03-15 11:52:05,185] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:05,186] [INFO] DFAST_QC result json was written to OceanDNA-a3147/dqc_result.json
[2023-03-15 11:52:05,186] [INFO] DFAST_QC completed!
[2023-03-15 11:52:05,186] [INFO] Total running time: 0h0m48s