[2023-03-18 08:55:50,668] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,668] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b92b54d-1f15-4351-a047-25fd9a44e783/dqc_reference
[2023-03-18 08:55:51,789] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,789] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,790] [INFO] Running command: cat /var/lib/cwl/stge928c4f6-cb5b-44bb-8dd6-045d5ea689f6/OceanDNA-b2112.fa | prodigal -d OceanDNA-b2112/cds.fna -a OceanDNA-b2112/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:55,306] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:55,306] [INFO] Task started: HMMsearch
[2023-03-18 08:55:55,306] [INFO] Running command: hmmsearch --tblout OceanDNA-b2112/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b92b54d-1f15-4351-a047-25fd9a44e783/dqc_reference/reference_markers.hmm OceanDNA-b2112/protein.faa > /dev/null
[2023-03-18 08:55:55,510] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:55,510] [INFO] Found 6/6 markers.
[2023-03-18 08:55:55,517] [INFO] Query marker FASTA was written to OceanDNA-b2112/markers.fasta
[2023-03-18 08:55:55,518] [INFO] Task started: Blastn
[2023-03-18 08:55:55,518] [INFO] Running command: blastn -query OceanDNA-b2112/markers.fasta -db /var/lib/cwl/stg7b92b54d-1f15-4351-a047-25fd9a44e783/dqc_reference/reference_markers.fasta -out OceanDNA-b2112/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:55:56,030] [INFO] Task succeeded: Blastn
[2023-03-18 08:55:56,031] [INFO] Selected 12 target genomes.
[2023-03-18 08:55:56,031] [INFO] Target genome list was writen to OceanDNA-b2112/target_genomes.txt
[2023-03-18 08:55:56,040] [INFO] Task started: fastANI
[2023-03-18 08:55:56,040] [INFO] Running command: fastANI --query /var/lib/cwl/stge928c4f6-cb5b-44bb-8dd6-045d5ea689f6/OceanDNA-b2112.fa --refList OceanDNA-b2112/target_genomes.txt --output OceanDNA-b2112/fastani_result.tsv --threads 1
[2023-03-18 08:56:01,710] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:01,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b92b54d-1f15-4351-a047-25fd9a44e783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:01,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b92b54d-1f15-4351-a047-25fd9a44e783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:01,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:01,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:56:01,710] [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 08:56:01,711] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2112/tc_result.tsv
[2023-03-18 08:56:01,711] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:01,711] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:01,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b92b54d-1f15-4351-a047-25fd9a44e783/dqc_reference/checkm_data
[2023-03-18 08:56:01,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:01,724] [INFO] Task started: CheckM
[2023-03-18 08:56:01,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2112/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2112/checkm_input OceanDNA-b2112/checkm_result
[2023-03-18 08:56:17,449] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:17,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:17,452] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:17,452] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:17,452] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2112/markers.fasta)
[2023-03-18 08:56:17,453] [INFO] Task started: Blastn
[2023-03-18 08:56:17,453] [INFO] Running command: blastn -query OceanDNA-b2112/markers.fasta -db /var/lib/cwl/stg7b92b54d-1f15-4351-a047-25fd9a44e783/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2112/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:18,240] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:18,241] [INFO] Selected 20 target genomes.
[2023-03-18 08:56:18,241] [INFO] Target genome list was writen to OceanDNA-b2112/target_genomes_gtdb.txt
[2023-03-18 08:56:18,293] [INFO] Task started: fastANI
[2023-03-18 08:56:18,293] [INFO] Running command: fastANI --query /var/lib/cwl/stge928c4f6-cb5b-44bb-8dd6-045d5ea689f6/OceanDNA-b2112.fa --refList OceanDNA-b2112/target_genomes_gtdb.txt --output OceanDNA-b2112/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:22,123] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:22,130] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:56:22,130] [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_014239265.1	s__Actinomarina sp014239265	82.5302	173	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510965.1	s__Actinomarina sp002683085	81.6329	123	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.49	98.44	0.76	0.76	3	-
GCA_002169845.1	s__Actinomarina sp002169845	80.758	105	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384285.1	s__Actinomarina sp014384285	80.2608	155	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	-
GCA_002169115.2	s__Actinomarina sp002169115	80.2593	70	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.47	96.47	0.52	0.52	2	-
GCA_002308095.1	s__Actinomarina sp002308095	79.7883	95	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282445.1	s__Actinomarina sp003282445	76.8123	73	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	-
GCA_902555985.1	s__Actinomarina sp902555985	76.7524	59	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.40	96.59	0.85	0.83	4	-
GCA_902519845.1	s__Actinomarina sp902519845	76.4706	50	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.50	95.50	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:22,131] [INFO] GTDB search result was written to OceanDNA-b2112/result_gtdb.tsv
[2023-03-18 08:56:22,132] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:22,133] [INFO] DFAST_QC result json was written to OceanDNA-b2112/dqc_result.json
[2023-03-18 08:56:22,133] [INFO] DFAST_QC completed!
[2023-03-18 08:56:22,133] [INFO] Total running time: 0h0m31s