[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg9973e7e1-159a-48e6-979c-55d318f7b7c6/dqc_reference
[2023-03-18 20:59:45,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,681] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,681] [INFO] Running command: cat /var/lib/cwl/stg14b404f9-b081-4b59-9677-c3c8879cb4b7/OceanDNA-a3040.fa | prodigal -d OceanDNA-a3040/cds.fna -a OceanDNA-a3040/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:57,483] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:57,484] [INFO] Task started: HMMsearch
[2023-03-18 20:59:57,484] [INFO] Running command: hmmsearch --tblout OceanDNA-a3040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9973e7e1-159a-48e6-979c-55d318f7b7c6/dqc_reference/reference_markers.hmm OceanDNA-a3040/protein.faa > /dev/null
[2023-03-18 20:59:57,696] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:57,696] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg14b404f9-b081-4b59-9677-c3c8879cb4b7/OceanDNA-a3040.fa]
[2023-03-18 20:59:57,708] [INFO] Query marker FASTA was written to OceanDNA-a3040/markers.fasta
[2023-03-18 20:59:57,709] [INFO] Task started: Blastn
[2023-03-18 20:59:57,709] [INFO] Running command: blastn -query OceanDNA-a3040/markers.fasta -db /var/lib/cwl/stg9973e7e1-159a-48e6-979c-55d318f7b7c6/dqc_reference/reference_markers.fasta -out OceanDNA-a3040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:58,152] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:58,153] [INFO] Selected 5 target genomes.
[2023-03-18 20:59:58,153] [INFO] Target genome list was writen to OceanDNA-a3040/target_genomes.txt
[2023-03-18 20:59:58,156] [INFO] Task started: fastANI
[2023-03-18 20:59:58,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg14b404f9-b081-4b59-9677-c3c8879cb4b7/OceanDNA-a3040.fa --refList OceanDNA-a3040/target_genomes.txt --output OceanDNA-a3040/fastani_result.tsv --threads 1
[2023-03-18 21:00:01,692] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:01,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9973e7e1-159a-48e6-979c-55d318f7b7c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:01,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9973e7e1-159a-48e6-979c-55d318f7b7c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:01,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:01,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:00:01,693] [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
--------------------------------------------------------------------------------
[2023-03-18 21:00:01,693] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3040/tc_result.tsv
[2023-03-18 21:00:01,693] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:01,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:01,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9973e7e1-159a-48e6-979c-55d318f7b7c6/dqc_reference/checkm_data
[2023-03-18 21:00:01,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:01,701] [INFO] Task started: CheckM
[2023-03-18 21:00:01,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3040/checkm_input OceanDNA-a3040/checkm_result
[2023-03-18 21:00:36,442] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:36,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:36,450] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:36,450] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:36,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3040/markers.fasta)
[2023-03-18 21:00:36,451] [INFO] Task started: Blastn
[2023-03-18 21:00:36,451] [INFO] Running command: blastn -query OceanDNA-a3040/markers.fasta -db /var/lib/cwl/stg9973e7e1-159a-48e6-979c-55d318f7b7c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:36,961] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:36,963] [INFO] Selected 7 target genomes.
[2023-03-18 21:00:36,963] [INFO] Target genome list was writen to OceanDNA-a3040/target_genomes_gtdb.txt
[2023-03-18 21:00:36,971] [INFO] Task started: fastANI
[2023-03-18 21:00:36,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg14b404f9-b081-4b59-9677-c3c8879cb4b7/OceanDNA-a3040.fa --refList OceanDNA-a3040/target_genomes_gtdb.txt --output OceanDNA-a3040/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:00:39,655] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:39,660] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:00:39,660] [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_002494645.1	s__Poseidonia sp002494645	99.9327	548	584	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.84	99.84	0.96	0.96	2	conclusive
GCA_016778305.1	s__Poseidonia sp016778305	81.7441	465	584	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.89	99.85	0.97	0.96	5	-
GCA_003602485.1	s__Poseidonia sp003602485	81.7066	402	584	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704515.1	s__Poseidonia sp002704515	77.2956	130	584	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495645.1	s__Poseidonia sp002495645	77.1761	144	584	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002694525.1	s__Poseidonia sp002694525	77.0213	98	584	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000246735.1	s__MGIIa-L1 sp000246735	76.9562	70	584	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.40	99.32	0.97	0.89	6	-
--------------------------------------------------------------------------------
[2023-03-18 21:00:39,663] [INFO] GTDB search result was written to OceanDNA-a3040/result_gtdb.tsv
[2023-03-18 21:00:39,665] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:00:39,669] [INFO] DFAST_QC result json was written to OceanDNA-a3040/dqc_result.json
[2023-03-18 21:00:39,669] [INFO] DFAST_QC completed!
[2023-03-18 21:00:39,669] [INFO] Total running time: 0h0m56s