[2023-06-30 05:19:03,716] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:19:03,719] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:19:03,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9372731-e6f0-4348-bfa6-75d77d4f796b/dqc_reference
[2023-06-30 05:19:04,992] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:19:04,993] [INFO] Task started: Prodigal
[2023-06-30 05:19:04,993] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bd821f3-5c9f-4d95-bf83-38be78ad1848/GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna.gz | prodigal -d GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/cds.fna -a GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:19:15,668] [INFO] Task succeeded: Prodigal
[2023-06-30 05:19:15,668] [INFO] Task started: HMMsearch
[2023-06-30 05:19:15,668] [INFO] Running command: hmmsearch --tblout GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9372731-e6f0-4348-bfa6-75d77d4f796b/dqc_reference/reference_markers.hmm GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:19:15,916] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:19:15,917] [INFO] Found 6/6 markers.
[2023-06-30 05:19:15,946] [INFO] Query marker FASTA was written to GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/markers.fasta
[2023-06-30 05:19:15,947] [INFO] Task started: Blastn
[2023-06-30 05:19:15,947] [INFO] Running command: blastn -query GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9372731-e6f0-4348-bfa6-75d77d4f796b/dqc_reference/reference_markers.fasta -out GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:19:16,528] [INFO] Task succeeded: Blastn
[2023-06-30 05:19:16,531] [INFO] Selected 13 target genomes.
[2023-06-30 05:19:16,532] [INFO] Target genome list was writen to GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/target_genomes.txt
[2023-06-30 05:19:16,533] [INFO] Task started: fastANI
[2023-06-30 05:19:16,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd821f3-5c9f-4d95-bf83-38be78ad1848/GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna.gz --refList GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/target_genomes.txt --output GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:19:23,437] [INFO] Task succeeded: fastANI
[2023-06-30 05:19:23,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9372731-e6f0-4348-bfa6-75d77d4f796b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:19:23,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9372731-e6f0-4348-bfa6-75d77d4f796b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:19:23,444] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:19:23,444] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:19:23,444] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	78.3495	251	652	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	78.0045	219	652	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	76.8689	124	652	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	76.6313	90	652	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:19:23,447] [INFO] DFAST Taxonomy check result was written to GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/tc_result.tsv
[2023-06-30 05:19:23,448] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:19:23,448] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:19:23,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9372731-e6f0-4348-bfa6-75d77d4f796b/dqc_reference/checkm_data
[2023-06-30 05:19:23,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:19:23,477] [INFO] Task started: CheckM
[2023-06-30 05:19:23,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/checkm_input GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/checkm_result
[2023-06-30 05:20:00,475] [INFO] Task succeeded: CheckM
[2023-06-30 05:20:00,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:20:00,496] [INFO] ===== Completeness check finished =====
[2023-06-30 05:20:00,496] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:20:00,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/markers.fasta)
[2023-06-30 05:20:00,497] [INFO] Task started: Blastn
[2023-06-30 05:20:00,497] [INFO] Running command: blastn -query GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9372731-e6f0-4348-bfa6-75d77d4f796b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:20:01,289] [INFO] Task succeeded: Blastn
[2023-06-30 05:20:01,294] [INFO] Selected 10 target genomes.
[2023-06-30 05:20:01,294] [INFO] Target genome list was writen to GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:20:01,301] [INFO] Task started: fastANI
[2023-06-30 05:20:01,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd821f3-5c9f-4d95-bf83-38be78ad1848/GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna.gz --refList GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/target_genomes_gtdb.txt --output GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:20:06,549] [INFO] Task succeeded: fastANI
[2023-06-30 05:20:06,563] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:20:06,563] [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_903895195.1	s__Chlorobium sp903895195	99.1237	589	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.65	0.92	0.86	65	conclusive
GCA_005843825.1	s__Chlorobium sp005843825	87.7908	509	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.19	97.55	0.89	0.82	50	-
GCA_903908555.1	s__Chlorobium sp903908555	87.4734	430	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.53	99.53	0.79	0.79	2	-
GCA_903851385.1	s__Chlorobium sp903851385	87.4132	518	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.86	99.82	0.97	0.97	3	-
GCA_903920215.1	s__Chlorobium sp903920215	87.2748	488	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904495.1	s__Chlorobium sp903904495	82.9706	316	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.87	98.87	0.74	0.74	2	-
GCA_012972825.1	s__Chlorobium sp012972825	82.3897	440	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903940125.1	s__Chlorobium sp903940125	82.0078	448	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.50	97.06	0.88	0.72	14	-
GCA_903869365.1	s__Chlorobium sp903869365	81.886	443	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.79	99.50	0.93	0.82	33	-
GCA_012972835.1	s__Chlorobium sp012972835	80.7641	418	652	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:20:06,565] [INFO] GTDB search result was written to GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/result_gtdb.tsv
[2023-06-30 05:20:06,566] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:20:06,569] [INFO] DFAST_QC result json was written to GCA_903830175.1_freshwater_MAG_---_MJ120716B_bin-429_genomic.fna/dqc_result.json
[2023-06-30 05:20:06,569] [INFO] DFAST_QC completed!
[2023-06-30 05:20:06,569] [INFO] Total running time: 0h1m3s