[2023-06-17 11:44:14,951] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:44:14,953] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:44:14,953] [INFO] DQC Reference Directory: /var/lib/cwl/stg7142dcfd-d1d5-4019-81ea-8c6b97890af8/dqc_reference
[2023-06-17 11:44:16,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:44:16,568] [INFO] Task started: Prodigal
[2023-06-17 11:44:16,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg9534148b-099c-48ba-9cc9-f49e07009e14/GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna.gz | prodigal -d GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/cds.fna -a GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:44:23,630] [INFO] Task succeeded: Prodigal
[2023-06-17 11:44:23,631] [INFO] Task started: HMMsearch
[2023-06-17 11:44:23,631] [INFO] Running command: hmmsearch --tblout GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7142dcfd-d1d5-4019-81ea-8c6b97890af8/dqc_reference/reference_markers.hmm GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:44:23,871] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:44:23,873] [INFO] Found 6/6 markers.
[2023-06-17 11:44:23,901] [INFO] Query marker FASTA was written to GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/markers.fasta
[2023-06-17 11:44:23,901] [INFO] Task started: Blastn
[2023-06-17 11:44:23,901] [INFO] Running command: blastn -query GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/markers.fasta -db /var/lib/cwl/stg7142dcfd-d1d5-4019-81ea-8c6b97890af8/dqc_reference/reference_markers.fasta -out GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:24,600] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:24,605] [INFO] Selected 23 target genomes.
[2023-06-17 11:44:24,606] [INFO] Target genome list was writen to GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/target_genomes.txt
[2023-06-17 11:44:24,612] [INFO] Task started: fastANI
[2023-06-17 11:44:24,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg9534148b-099c-48ba-9cc9-f49e07009e14/GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna.gz --refList GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/target_genomes.txt --output GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:44:36,643] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:36,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7142dcfd-d1d5-4019-81ea-8c6b97890af8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:44:36,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7142dcfd-d1d5-4019-81ea-8c6b97890af8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:44:36,668] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:44:36,668] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:44:36,668] [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
Acutalibacter muris	strain=KB18	GCA_002201475.1	1796620	1796620	type	True	78.1344	240	721	95	below_threshold
Acutalibacter muris	strain=KB18	GCA_016697365.1	1796620	1796620	type	True	78.0215	242	721	95	below_threshold
Neglectibacter timonensis	strain=SN17	GCA_900048895.1	1776382	1776382	type	True	77.9394	169	721	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	77.6004	120	721	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.0201	67	721	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.9264	104	721	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.9026	84	721	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.7818	68	721	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.755	73	721	95	below_threshold
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	76.5228	59	721	95	below_threshold
Phocea massiliensis	strain=Marseille-P2769	GCA_900104615.1	1841867	1841867	type	True	76.4994	76	721	95	below_threshold
Hydrogeniiclostridium mannosilyticum	strain=ASD2818	GCA_003268275.1	2764322	2764322	type	True	76.4797	58	721	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:44:36,671] [INFO] DFAST Taxonomy check result was written to GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/tc_result.tsv
[2023-06-17 11:44:36,672] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:44:36,672] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:44:36,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7142dcfd-d1d5-4019-81ea-8c6b97890af8/dqc_reference/checkm_data
[2023-06-17 11:44:36,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:44:36,706] [INFO] Task started: CheckM
[2023-06-17 11:44:36,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/checkm_input GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/checkm_result
[2023-06-17 11:45:01,851] [INFO] Task succeeded: CheckM
[2023-06-17 11:45:01,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:45:01,875] [INFO] ===== Completeness check finished =====
[2023-06-17 11:45:01,875] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:45:01,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/markers.fasta)
[2023-06-17 11:45:01,876] [INFO] Task started: Blastn
[2023-06-17 11:45:01,876] [INFO] Running command: blastn -query GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/markers.fasta -db /var/lib/cwl/stg7142dcfd-d1d5-4019-81ea-8c6b97890af8/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:45:03,106] [INFO] Task succeeded: Blastn
[2023-06-17 11:45:03,111] [INFO] Selected 9 target genomes.
[2023-06-17 11:45:03,111] [INFO] Target genome list was writen to GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:45:03,121] [INFO] Task started: fastANI
[2023-06-17 11:45:03,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg9534148b-099c-48ba-9cc9-f49e07009e14/GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna.gz --refList GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/target_genomes_gtdb.txt --output GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:45:08,013] [INFO] Task succeeded: fastANI
[2023-06-17 11:45:08,030] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:45:08,031] [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_000435395.1	s__Acutalibacter ornithocaccae	98.0746	598	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.90	97.28	0.83	0.80	5	conclusive
GCA_900543555.1	s__Acutalibacter stercoravium	85.8367	492	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.18	97.66	0.89	0.84	11	-
GCA_905215055.1	s__Acutalibacter sp905215055	84.9757	525	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904374805.1	s__Acutalibacter sp904374805	82.9316	470	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.85	98.27	0.91	0.86	5	-
GCA_900548545.1	s__Acutalibacter sp900548545	82.3405	418	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.53	98.53	0.88	0.88	2	-
GCA_904391645.1	s__Acutalibacter sp904391645	82.3055	352	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900755895.1	s__Acutalibacter sp900755895	80.9842	402	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	96.98	96.98	0.93	0.93	2	-
GCA_000432995.1	s__Acutalibacter sp000432995	80.9136	438	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.39	97.36	0.87	0.86	3	-
GCA_900759575.1	s__Acutalibacter sp900759575	79.8751	262	721	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:45:08,033] [INFO] GTDB search result was written to GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/result_gtdb.tsv
[2023-06-17 11:45:08,035] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:45:08,040] [INFO] DFAST_QC result json was written to GCA_905201625.1_SRR2912783-mag-bin.8_genomic.fna/dqc_result.json
[2023-06-17 11:45:08,040] [INFO] DFAST_QC completed!
[2023-06-17 11:45:08,040] [INFO] Total running time: 0h0m53s