[2023-06-17 15:05:51,816] [INFO] DFAST_QC pipeline started.
[2023-06-17 15:05:51,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 15:05:51,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg47ee4856-d825-4d51-bdee-cd64d29e3270/dqc_reference
[2023-06-17 15:05:54,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 15:05:54,125] [INFO] Task started: Prodigal
[2023-06-17 15:05:54,125] [INFO] Running command: gunzip -c /var/lib/cwl/stg74fc177c-7199-43b8-ad23-c42d12d7011b/GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna.gz | prodigal -d GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/cds.fna -a GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 15:05:59,040] [INFO] Task succeeded: Prodigal
[2023-06-17 15:05:59,041] [INFO] Task started: HMMsearch
[2023-06-17 15:05:59,041] [INFO] Running command: hmmsearch --tblout GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47ee4856-d825-4d51-bdee-cd64d29e3270/dqc_reference/reference_markers.hmm GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/protein.faa > /dev/null
[2023-06-17 15:05:59,281] [INFO] Task succeeded: HMMsearch
[2023-06-17 15:05:59,283] [INFO] Found 6/6 markers.
[2023-06-17 15:05:59,308] [INFO] Query marker FASTA was written to GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/markers.fasta
[2023-06-17 15:05:59,309] [INFO] Task started: Blastn
[2023-06-17 15:05:59,309] [INFO] Running command: blastn -query GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stg47ee4856-d825-4d51-bdee-cd64d29e3270/dqc_reference/reference_markers.fasta -out GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:05:59,884] [INFO] Task succeeded: Blastn
[2023-06-17 15:05:59,887] [INFO] Selected 21 target genomes.
[2023-06-17 15:05:59,888] [INFO] Target genome list was writen to GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/target_genomes.txt
[2023-06-17 15:05:59,894] [INFO] Task started: fastANI
[2023-06-17 15:05:59,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg74fc177c-7199-43b8-ad23-c42d12d7011b/GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna.gz --refList GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/target_genomes.txt --output GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 15:06:08,865] [INFO] Task succeeded: fastANI
[2023-06-17 15:06:08,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47ee4856-d825-4d51-bdee-cd64d29e3270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 15:06:08,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47ee4856-d825-4d51-bdee-cd64d29e3270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 15:06:08,868] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 15:06:08,868] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 15:06:08,868] [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
--------------------------------------------------------------------------------
[2023-06-17 15:06:08,871] [INFO] DFAST Taxonomy check result was written to GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/tc_result.tsv
[2023-06-17 15:06:08,872] [INFO] ===== Taxonomy check completed =====
[2023-06-17 15:06:08,872] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 15:06:08,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47ee4856-d825-4d51-bdee-cd64d29e3270/dqc_reference/checkm_data
[2023-06-17 15:06:08,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 15:06:08,900] [INFO] Task started: CheckM
[2023-06-17 15:06:08,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/checkm_input GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/checkm_result
[2023-06-17 15:06:30,280] [INFO] Task succeeded: CheckM
[2023-06-17 15:06:30,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 15:06:30,304] [INFO] ===== Completeness check finished =====
[2023-06-17 15:06:30,304] [INFO] ===== Start GTDB Search =====
[2023-06-17 15:06:30,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/markers.fasta)
[2023-06-17 15:06:30,305] [INFO] Task started: Blastn
[2023-06-17 15:06:30,305] [INFO] Running command: blastn -query GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stg47ee4856-d825-4d51-bdee-cd64d29e3270/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:06:31,106] [INFO] Task succeeded: Blastn
[2023-06-17 15:06:31,111] [INFO] Selected 18 target genomes.
[2023-06-17 15:06:31,112] [INFO] Target genome list was writen to GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 15:06:31,127] [INFO] Task started: fastANI
[2023-06-17 15:06:31,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg74fc177c-7199-43b8-ad23-c42d12d7011b/GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna.gz --refList GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/target_genomes_gtdb.txt --output GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 15:06:37,448] [INFO] Task succeeded: fastANI
[2023-06-17 15:06:37,460] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 15:06:37,460] [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_000980375.1	s__Limenecus avicola	98.6525	642	684	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Limenecus	95.0	98.45	97.78	0.95	0.92	8	conclusive
GCA_018362895.1	s__Limenecus sp018362895	79.0349	292	684	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Limenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547155.1	s__Spyradomonas excrementavium	78.4785	147	684	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Spyradomonas	95.0	99.06	98.43	0.95	0.94	4	-
GCA_900547585.1	s__Spyradomonas sp900547585	77.8189	105	684	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Spyradomonas	95.0	99.89	99.89	0.88	0.88	2	-
GCA_910588555.1	s__Stercorousia sp910588555	77.2277	59	684	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551915.1	s__Scatenecus faecavium	76.536	66	684	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatenecus	95.0	98.79	98.66	0.89	0.87	5	-
GCA_017409065.1	s__RGIG2134 sp017409065	76.3423	58	684	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__RGIG2134	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 15:06:37,463] [INFO] GTDB search result was written to GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/result_gtdb.tsv
[2023-06-17 15:06:37,463] [INFO] ===== GTDB Search completed =====
[2023-06-17 15:06:37,466] [INFO] DFAST_QC result json was written to GCA_905207335.1_ERR2824912-mag-bin.16_genomic.fna/dqc_result.json
[2023-06-17 15:06:37,467] [INFO] DFAST_QC completed!
[2023-06-17 15:06:37,467] [INFO] Total running time: 0h0m46s