[2023-03-16 05:50:18,332] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:50:18,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:50:18,332] [INFO] DQC Reference Directory: /var/lib/cwl/stgca90b96a-21fe-4410-be21-8886d061fd08/dqc_reference
[2023-03-16 05:50:20,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:50:20,129] [INFO] Task started: Prodigal
[2023-03-16 05:50:20,129] [INFO] Running command: cat /var/lib/cwl/stg020bd146-cb69-4648-a0b6-f5f35e88c34d/OceanDNA-a3050.fa | prodigal -d OceanDNA-a3050/cds.fna -a OceanDNA-a3050/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:50:31,813] [INFO] Task succeeded: Prodigal
[2023-03-16 05:50:31,813] [INFO] Task started: HMMsearch
[2023-03-16 05:50:31,813] [INFO] Running command: hmmsearch --tblout OceanDNA-a3050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca90b96a-21fe-4410-be21-8886d061fd08/dqc_reference/reference_markers.hmm OceanDNA-a3050/protein.faa > /dev/null
[2023-03-16 05:50:31,979] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:50:31,979] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg020bd146-cb69-4648-a0b6-f5f35e88c34d/OceanDNA-a3050.fa]
[2023-03-16 05:50:31,992] [INFO] Query marker FASTA was written to OceanDNA-a3050/markers.fasta
[2023-03-16 05:50:31,993] [INFO] Task started: Blastn
[2023-03-16 05:50:31,993] [INFO] Running command: blastn -query OceanDNA-a3050/markers.fasta -db /var/lib/cwl/stgca90b96a-21fe-4410-be21-8886d061fd08/dqc_reference/reference_markers.fasta -out OceanDNA-a3050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:50:32,416] [INFO] Task succeeded: Blastn
[2023-03-16 05:50:32,417] [INFO] Selected 5 target genomes.
[2023-03-16 05:50:32,417] [INFO] Target genome list was writen to OceanDNA-a3050/target_genomes.txt
[2023-03-16 05:50:32,421] [INFO] Task started: fastANI
[2023-03-16 05:50:32,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg020bd146-cb69-4648-a0b6-f5f35e88c34d/OceanDNA-a3050.fa --refList OceanDNA-a3050/target_genomes.txt --output OceanDNA-a3050/fastani_result.tsv --threads 1
[2023-03-16 05:50:35,527] [INFO] Task succeeded: fastANI
[2023-03-16 05:50:35,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca90b96a-21fe-4410-be21-8886d061fd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:50:35,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca90b96a-21fe-4410-be21-8886d061fd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:50:35,528] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:50:35,528] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:50:35,528] [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
--------------------------------------------------------------------------------
[2023-03-16 05:50:35,528] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3050/tc_result.tsv
[2023-03-16 05:50:35,528] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:50:35,528] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:50:35,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca90b96a-21fe-4410-be21-8886d061fd08/dqc_reference/checkm_data
[2023-03-16 05:50:35,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:50:35,695] [INFO] Task started: CheckM
[2023-03-16 05:50:35,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3050/checkm_input OceanDNA-a3050/checkm_result
[2023-03-16 05:51:13,559] [INFO] Task succeeded: CheckM
[2023-03-16 05:51:13,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:51:13,561] [INFO] ===== Completeness check finished =====
[2023-03-16 05:51:13,561] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:51:13,561] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3050/markers.fasta)
[2023-03-16 05:51:13,562] [INFO] Task started: Blastn
[2023-03-16 05:51:13,562] [INFO] Running command: blastn -query OceanDNA-a3050/markers.fasta -db /var/lib/cwl/stgca90b96a-21fe-4410-be21-8886d061fd08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:51:13,999] [INFO] Task succeeded: Blastn
[2023-03-16 05:51:14,000] [INFO] Selected 10 target genomes.
[2023-03-16 05:51:14,000] [INFO] Target genome list was writen to OceanDNA-a3050/target_genomes_gtdb.txt
[2023-03-16 05:51:14,006] [INFO] Task started: fastANI
[2023-03-16 05:51:14,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg020bd146-cb69-4648-a0b6-f5f35e88c34d/OceanDNA-a3050.fa --refList OceanDNA-a3050/target_genomes_gtdb.txt --output OceanDNA-a3050/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:51:17,751] [INFO] Task succeeded: fastANI
[2023-03-16 05:51:17,757] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:51:17,758] [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_002497765.1	s__Poseidonia sp002497765	99.5367	486	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.70	99.65	0.88	0.86	3	conclusive
GCA_002725275.1	s__Poseidonia sp002725275	81.6263	332	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_002495645.1	s__Poseidonia sp002495645	80.055	317	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002689105.1	s__Poseidonia sp002689105	79.9084	257	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_002694525.1	s__Poseidonia sp002694525	78.9975	224	564	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	78.945	242	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_002704515.1	s__Poseidonia sp002704515	78.6837	236	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779705.1	s__Poseidonia sp016779705	78.4187	196	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722695.1	s__Poseidonia sp002722695	78.2272	235	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_002722135.1	s__MGIIa-L3 sp002722135	76.8887	74	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.74	99.72	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-16 05:51:17,758] [INFO] GTDB search result was written to OceanDNA-a3050/result_gtdb.tsv
[2023-03-16 05:51:17,758] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:51:17,759] [INFO] DFAST_QC result json was written to OceanDNA-a3050/dqc_result.json
[2023-03-16 05:51:17,759] [INFO] DFAST_QC completed!
[2023-03-16 05:51:17,759] [INFO] Total running time: 0h0m59s