[2023-03-16 10:13:36,010] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:13:36,010] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:13:36,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg002bfba9-cbe3-478e-868e-2df09df11e13/dqc_reference
[2023-03-16 10:13:37,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:13:37,157] [INFO] Task started: Prodigal
[2023-03-16 10:13:37,157] [INFO] Running command: cat /var/lib/cwl/stg09e959cb-5bb6-41d8-866a-7e3df61ccd03/OceanDNA-b18014.fa | prodigal -d OceanDNA-b18014/cds.fna -a OceanDNA-b18014/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:13:39,144] [INFO] Task succeeded: Prodigal
[2023-03-16 10:13:39,144] [INFO] Task started: HMMsearch
[2023-03-16 10:13:39,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b18014/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg002bfba9-cbe3-478e-868e-2df09df11e13/dqc_reference/reference_markers.hmm OceanDNA-b18014/protein.faa > /dev/null
[2023-03-16 10:13:39,272] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:13:39,272] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg09e959cb-5bb6-41d8-866a-7e3df61ccd03/OceanDNA-b18014.fa]
[2023-03-16 10:13:39,278] [INFO] Query marker FASTA was written to OceanDNA-b18014/markers.fasta
[2023-03-16 10:13:39,280] [INFO] Task started: Blastn
[2023-03-16 10:13:39,280] [INFO] Running command: blastn -query OceanDNA-b18014/markers.fasta -db /var/lib/cwl/stg002bfba9-cbe3-478e-868e-2df09df11e13/dqc_reference/reference_markers.fasta -out OceanDNA-b18014/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:13:39,792] [INFO] Task succeeded: Blastn
[2023-03-16 10:13:39,793] [INFO] Selected 15 target genomes.
[2023-03-16 10:13:39,793] [INFO] Target genome list was writen to OceanDNA-b18014/target_genomes.txt
[2023-03-16 10:13:39,906] [INFO] Task started: fastANI
[2023-03-16 10:13:39,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e959cb-5bb6-41d8-866a-7e3df61ccd03/OceanDNA-b18014.fa --refList OceanDNA-b18014/target_genomes.txt --output OceanDNA-b18014/fastani_result.tsv --threads 1
[2023-03-16 10:13:45,122] [INFO] Task succeeded: fastANI
[2023-03-16 10:13:45,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg002bfba9-cbe3-478e-868e-2df09df11e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:13:45,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg002bfba9-cbe3-478e-868e-2df09df11e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:13:45,123] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:13:45,123] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:13:45,123] [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 10:13:45,124] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18014/tc_result.tsv
[2023-03-16 10:13:45,124] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:13:45,124] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:13:45,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg002bfba9-cbe3-478e-868e-2df09df11e13/dqc_reference/checkm_data
[2023-03-16 10:13:45,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:13:45,517] [INFO] Task started: CheckM
[2023-03-16 10:13:45,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18014/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18014/checkm_input OceanDNA-b18014/checkm_result
[2023-03-16 10:14:00,497] [INFO] Task succeeded: CheckM
[2023-03-16 10:14:00,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:14:00,500] [INFO] ===== Completeness check finished =====
[2023-03-16 10:14:00,500] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:14:00,500] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18014/markers.fasta)
[2023-03-16 10:14:00,501] [INFO] Task started: Blastn
[2023-03-16 10:14:00,501] [INFO] Running command: blastn -query OceanDNA-b18014/markers.fasta -db /var/lib/cwl/stg002bfba9-cbe3-478e-868e-2df09df11e13/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18014/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:14:01,084] [INFO] Task succeeded: Blastn
[2023-03-16 10:14:01,086] [INFO] Selected 14 target genomes.
[2023-03-16 10:14:01,086] [INFO] Target genome list was writen to OceanDNA-b18014/target_genomes_gtdb.txt
[2023-03-16 10:14:01,128] [INFO] Task started: fastANI
[2023-03-16 10:14:01,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e959cb-5bb6-41d8-866a-7e3df61ccd03/OceanDNA-b18014.fa --refList OceanDNA-b18014/target_genomes_gtdb.txt --output OceanDNA-b18014/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:14:03,610] [INFO] Task succeeded: fastANI
[2023-03-16 10:14:03,613] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:14:03,614] [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_012963075.1	s__Marinisoma sp012963075	89.3007	78	110	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902575395.1	s__Marinisoma sp902575395	80.6673	73	110	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002348725.1	s__Marinisoma sp002348725	80.5318	67	110	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.66	99.62	0.84	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-16 10:14:03,614] [INFO] GTDB search result was written to OceanDNA-b18014/result_gtdb.tsv
[2023-03-16 10:14:03,614] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:14:03,616] [INFO] DFAST_QC result json was written to OceanDNA-b18014/dqc_result.json
[2023-03-16 10:14:03,616] [INFO] DFAST_QC completed!
[2023-03-16 10:14:03,616] [INFO] Total running time: 0h0m28s