[2023-03-17 10:48:45,547] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,547] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgda8bde6c-e425-475f-b41b-fd6b0fdefae9/dqc_reference
[2023-03-17 10:48:46,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,694] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,694] [INFO] Running command: cat /var/lib/cwl/stga0e8d58f-60a8-43d9-8142-9c9c1b522d64/OceanDNA-a2733.fa | prodigal -d OceanDNA-a2733/cds.fna -a OceanDNA-a2733/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:54,145] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:54,145] [INFO] Task started: HMMsearch
[2023-03-17 10:48:54,145] [INFO] Running command: hmmsearch --tblout OceanDNA-a2733/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda8bde6c-e425-475f-b41b-fd6b0fdefae9/dqc_reference/reference_markers.hmm OceanDNA-a2733/protein.faa > /dev/null
[2023-03-17 10:48:54,357] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:54,358] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga0e8d58f-60a8-43d9-8142-9c9c1b522d64/OceanDNA-a2733.fa]
[2023-03-17 10:48:54,371] [INFO] Query marker FASTA was written to OceanDNA-a2733/markers.fasta
[2023-03-17 10:48:54,373] [INFO] Task started: Blastn
[2023-03-17 10:48:54,373] [INFO] Running command: blastn -query OceanDNA-a2733/markers.fasta -db /var/lib/cwl/stgda8bde6c-e425-475f-b41b-fd6b0fdefae9/dqc_reference/reference_markers.fasta -out OceanDNA-a2733/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:55,038] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:55,039] [INFO] Selected 5 target genomes.
[2023-03-17 10:48:55,039] [INFO] Target genome list was writen to OceanDNA-a2733/target_genomes.txt
[2023-03-17 10:48:55,043] [INFO] Task started: fastANI
[2023-03-17 10:48:55,043] [INFO] Running command: fastANI --query /var/lib/cwl/stga0e8d58f-60a8-43d9-8142-9c9c1b522d64/OceanDNA-a2733.fa --refList OceanDNA-a2733/target_genomes.txt --output OceanDNA-a2733/fastani_result.tsv --threads 1
[2023-03-17 10:48:57,314] [INFO] Task succeeded: fastANI
[2023-03-17 10:48:57,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda8bde6c-e425-475f-b41b-fd6b0fdefae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:48:57,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda8bde6c-e425-475f-b41b-fd6b0fdefae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:48:57,315] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:48:57,315] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:48:57,315] [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 10:48:57,316] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2733/tc_result.tsv
[2023-03-17 10:48:57,316] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:48:57,316] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:48:57,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda8bde6c-e425-475f-b41b-fd6b0fdefae9/dqc_reference/checkm_data
[2023-03-17 10:48:57,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:48:57,322] [INFO] Task started: CheckM
[2023-03-17 10:48:57,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2733/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2733/checkm_input OceanDNA-a2733/checkm_result
[2023-03-17 10:49:23,041] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:23,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:23,044] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:23,044] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:23,045] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2733/markers.fasta)
[2023-03-17 10:49:23,045] [INFO] Task started: Blastn
[2023-03-17 10:49:23,045] [INFO] Running command: blastn -query OceanDNA-a2733/markers.fasta -db /var/lib/cwl/stgda8bde6c-e425-475f-b41b-fd6b0fdefae9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2733/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:23,525] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:23,526] [INFO] Selected 10 target genomes.
[2023-03-17 10:49:23,526] [INFO] Target genome list was writen to OceanDNA-a2733/target_genomes_gtdb.txt
[2023-03-17 10:49:23,659] [INFO] Task started: fastANI
[2023-03-17 10:49:23,660] [INFO] Running command: fastANI --query /var/lib/cwl/stga0e8d58f-60a8-43d9-8142-9c9c1b522d64/OceanDNA-a2733.fa --refList OceanDNA-a2733/target_genomes_gtdb.txt --output OceanDNA-a2733/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:26,758] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:26,765] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:49:26,765] [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_012270265.1	s__MGIIa-L2 sp012270265	95.7264	266	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018623995.1	s__MGIIa-L2 sp018623995	91.4297	292	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692685.1	s__MGIIa-L2 sp002692685	90.1648	203	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013330015.1	s__MGIIa-L2 sp8574u	88.6094	222	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002719815.1	s__MGIIa-L2 sp002719815	79.4553	180	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911465.1	s__MGIIa-L2 sp013911465	78.5647	135	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722615.1	s__MGIIa-L2 sp002722615	78.2612	168	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_002706065.1	s__MGIIa-L2 sp002706065	78.0741	190	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726845.1	s__MGIIa-L2 sp002726845	77.3478	101	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.43	97.43	0.74	0.74	2	-
GCA_018666575.1	s__MGIIa-L2 sp018666575	77.0935	68	361	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:26,766] [INFO] GTDB search result was written to OceanDNA-a2733/result_gtdb.tsv
[2023-03-17 10:49:26,766] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:26,767] [INFO] DFAST_QC result json was written to OceanDNA-a2733/dqc_result.json
[2023-03-17 10:49:26,767] [INFO] DFAST_QC completed!
[2023-03-17 10:49:26,767] [INFO] Total running time: 0h0m41s