[2023-03-16 17:04:01,086] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:04:01,087] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:04:01,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg79a0ba09-bd66-408b-b179-a9e5ad935e46/dqc_reference
[2023-03-16 17:04:02,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:04:02,315] [INFO] Task started: Prodigal
[2023-03-16 17:04:02,315] [INFO] Running command: cat /var/lib/cwl/stg8ac774f4-9b27-4b58-bf27-8c30aade6617/OceanDNA-b17430.fa | prodigal -d OceanDNA-b17430/cds.fna -a OceanDNA-b17430/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:04:19,748] [INFO] Task succeeded: Prodigal
[2023-03-16 17:04:19,748] [INFO] Task started: HMMsearch
[2023-03-16 17:04:19,748] [INFO] Running command: hmmsearch --tblout OceanDNA-b17430/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79a0ba09-bd66-408b-b179-a9e5ad935e46/dqc_reference/reference_markers.hmm OceanDNA-b17430/protein.faa > /dev/null
[2023-03-16 17:04:19,946] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:04:19,946] [INFO] Found 6/6 markers.
[2023-03-16 17:04:19,963] [INFO] Query marker FASTA was written to OceanDNA-b17430/markers.fasta
[2023-03-16 17:04:19,964] [INFO] Task started: Blastn
[2023-03-16 17:04:19,964] [INFO] Running command: blastn -query OceanDNA-b17430/markers.fasta -db /var/lib/cwl/stg79a0ba09-bd66-408b-b179-a9e5ad935e46/dqc_reference/reference_markers.fasta -out OceanDNA-b17430/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:04:20,505] [INFO] Task succeeded: Blastn
[2023-03-16 17:04:20,506] [INFO] Selected 29 target genomes.
[2023-03-16 17:04:20,506] [INFO] Target genome list was writen to OceanDNA-b17430/target_genomes.txt
[2023-03-16 17:04:20,683] [INFO] Task started: fastANI
[2023-03-16 17:04:20,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ac774f4-9b27-4b58-bf27-8c30aade6617/OceanDNA-b17430.fa --refList OceanDNA-b17430/target_genomes.txt --output OceanDNA-b17430/fastani_result.tsv --threads 1
[2023-03-16 17:04:45,928] [INFO] Task succeeded: fastANI
[2023-03-16 17:04:45,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79a0ba09-bd66-408b-b179-a9e5ad935e46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:04:45,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79a0ba09-bd66-408b-b179-a9e5ad935e46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:04:45,929] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:04:45,929] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:04:45,929] [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 17:04:45,929] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17430/tc_result.tsv
[2023-03-16 17:04:45,929] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:04:45,930] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:04:45,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79a0ba09-bd66-408b-b179-a9e5ad935e46/dqc_reference/checkm_data
[2023-03-16 17:04:45,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:04:45,937] [INFO] Task started: CheckM
[2023-03-16 17:04:45,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17430/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17430/checkm_input OceanDNA-b17430/checkm_result
[2023-03-16 17:05:48,782] [INFO] Task succeeded: CheckM
[2023-03-16 17:05:48,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:05:48,785] [INFO] ===== Completeness check finished =====
[2023-03-16 17:05:48,786] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:05:48,786] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17430/markers.fasta)
[2023-03-16 17:05:48,787] [INFO] Task started: Blastn
[2023-03-16 17:05:48,787] [INFO] Running command: blastn -query OceanDNA-b17430/markers.fasta -db /var/lib/cwl/stg79a0ba09-bd66-408b-b179-a9e5ad935e46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17430/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:05:49,807] [INFO] Task succeeded: Blastn
[2023-03-16 17:05:49,809] [INFO] Selected 30 target genomes.
[2023-03-16 17:05:49,809] [INFO] Target genome list was writen to OceanDNA-b17430/target_genomes_gtdb.txt
[2023-03-16 17:05:49,996] [INFO] Task started: fastANI
[2023-03-16 17:05:49,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ac774f4-9b27-4b58-bf27-8c30aade6617/OceanDNA-b17430.fa --refList OceanDNA-b17430/target_genomes_gtdb.txt --output OceanDNA-b17430/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:06:06,466] [INFO] Task succeeded: fastANI
[2023-03-16 17:06:06,469] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:06:06,470] [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_002712565.1	s__UBA822 sp002712565	78.0006	169	938	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA822	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731735.1	s__UBA822 sp002731735	77.9203	258	938	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA822	95.0	97.30	96.95	0.68	0.67	5	-
GCA_015664885.1	s__UBA1138 sp003447875	76.9159	65	938	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_009692205.1	s__UBA2982 sp009692205	75.8487	69	938	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873995.1	s__UBA2982 sp016873995	75.5734	66	938	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:06:06,471] [INFO] GTDB search result was written to OceanDNA-b17430/result_gtdb.tsv
[2023-03-16 17:06:06,471] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:06:06,472] [INFO] DFAST_QC result json was written to OceanDNA-b17430/dqc_result.json
[2023-03-16 17:06:06,472] [INFO] DFAST_QC completed!
[2023-03-16 17:06:06,472] [INFO] Total running time: 0h2m5s