[2023-03-14 12:56:04,173] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:56:04,174] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:56:04,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg489c0be4-affd-465a-9f41-359b4f1d62fb/dqc_reference
[2023-03-14 12:56:05,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:56:05,351] [INFO] Task started: Prodigal
[2023-03-14 12:56:05,351] [INFO] Running command: cat /var/lib/cwl/stg371a4378-8e0d-4440-8493-0a906eb22648/OceanDNA-a3121.fa | prodigal -d OceanDNA-a3121/cds.fna -a OceanDNA-a3121/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:56:16,632] [INFO] Task succeeded: Prodigal
[2023-03-14 12:56:16,632] [INFO] Task started: HMMsearch
[2023-03-14 12:56:16,632] [INFO] Running command: hmmsearch --tblout OceanDNA-a3121/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg489c0be4-affd-465a-9f41-359b4f1d62fb/dqc_reference/reference_markers.hmm OceanDNA-a3121/protein.faa > /dev/null
[2023-03-14 12:56:16,789] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:56:16,789] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg371a4378-8e0d-4440-8493-0a906eb22648/OceanDNA-a3121.fa]
[2023-03-14 12:56:16,803] [INFO] Query marker FASTA was written to OceanDNA-a3121/markers.fasta
[2023-03-14 12:56:16,805] [INFO] Task started: Blastn
[2023-03-14 12:56:16,805] [INFO] Running command: blastn -query OceanDNA-a3121/markers.fasta -db /var/lib/cwl/stg489c0be4-affd-465a-9f41-359b4f1d62fb/dqc_reference/reference_markers.fasta -out OceanDNA-a3121/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:56:17,232] [INFO] Task succeeded: Blastn
[2023-03-14 12:56:17,233] [INFO] Selected 8 target genomes.
[2023-03-14 12:56:17,233] [INFO] Target genome list was writen to OceanDNA-a3121/target_genomes.txt
[2023-03-14 12:56:17,237] [INFO] Task started: fastANI
[2023-03-14 12:56:17,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg371a4378-8e0d-4440-8493-0a906eb22648/OceanDNA-a3121.fa --refList OceanDNA-a3121/target_genomes.txt --output OceanDNA-a3121/fastani_result.tsv --threads 1
[2023-03-14 12:56:22,304] [INFO] Task succeeded: fastANI
[2023-03-14 12:56:22,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg489c0be4-affd-465a-9f41-359b4f1d62fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:56:22,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg489c0be4-affd-465a-9f41-359b4f1d62fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:56:22,304] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:56:22,304] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:56:22,304] [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
--------------------------------------------------------------------------------
[2023-03-14 12:56:22,305] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3121/tc_result.tsv
[2023-03-14 12:56:22,305] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:56:22,305] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:56:22,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg489c0be4-affd-465a-9f41-359b4f1d62fb/dqc_reference/checkm_data
[2023-03-14 12:56:22,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:56:22,312] [INFO] Task started: CheckM
[2023-03-14 12:56:22,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3121/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3121/checkm_input OceanDNA-a3121/checkm_result
[2023-03-14 12:56:57,260] [INFO] Task succeeded: CheckM
[2023-03-14 12:56:57,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:56:57,263] [INFO] ===== Completeness check finished =====
[2023-03-14 12:56:57,263] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:56:57,263] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3121/markers.fasta)
[2023-03-14 12:56:57,265] [INFO] Task started: Blastn
[2023-03-14 12:56:57,265] [INFO] Running command: blastn -query OceanDNA-a3121/markers.fasta -db /var/lib/cwl/stg489c0be4-affd-465a-9f41-359b4f1d62fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3121/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:56:58,705] [INFO] Task succeeded: Blastn
[2023-03-14 12:56:58,706] [INFO] Selected 11 target genomes.
[2023-03-14 12:56:58,706] [INFO] Target genome list was writen to OceanDNA-a3121/target_genomes_gtdb.txt
[2023-03-14 12:56:58,717] [INFO] Task started: fastANI
[2023-03-14 12:56:58,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg371a4378-8e0d-4440-8493-0a906eb22648/OceanDNA-a3121.fa --refList OceanDNA-a3121/target_genomes_gtdb.txt --output OceanDNA-a3121/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:57:05,042] [INFO] Task succeeded: fastANI
[2023-03-14 12:57:05,047] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:57:05,048] [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_002714305.1	s__Poseidonia sp002714305	98.6755	400	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	conclusive
GCA_002704515.1	s__Poseidonia sp002704515	87.2939	390	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002502295.1	s__Poseidonia sp002502295	81.034	367	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689105.1	s__Poseidonia sp002689105	79.1715	216	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_002725275.1	s__Poseidonia sp002725275	78.6923	226	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_002728035.1	s__Poseidonia sp002728035	77.9093	168	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.50	96.50	0.78	0.78	2	-
GCA_002505405.1	s__Poseidonia alphae	76.7464	89	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.19	99.15	0.93	0.90	5	-
GCA_013329255.1	s__MGIIa-L1 sp9513u	76.6149	59	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:57:05,048] [INFO] GTDB search result was written to OceanDNA-a3121/result_gtdb.tsv
[2023-03-14 12:57:05,048] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:57:05,049] [INFO] DFAST_QC result json was written to OceanDNA-a3121/dqc_result.json
[2023-03-14 12:57:05,049] [INFO] DFAST_QC completed!
[2023-03-14 12:57:05,049] [INFO] Total running time: 0h1m1s