[2023-06-29 13:04:19,253] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:04:19,256] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:04:19,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg922ff91f-2535-408f-9726-9c498aa70da8/dqc_reference
[2023-06-29 13:04:20,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:04:20,550] [INFO] Task started: Prodigal
[2023-06-29 13:04:20,550] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cb70099-15de-451b-a325-f175a71ea0ac/GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:04:24,096] [INFO] Task succeeded: Prodigal
[2023-06-29 13:04:24,096] [INFO] Task started: HMMsearch
[2023-06-29 13:04:24,097] [INFO] Running command: hmmsearch --tblout GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg922ff91f-2535-408f-9726-9c498aa70da8/dqc_reference/reference_markers.hmm GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:04:24,309] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:04:24,311] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7cb70099-15de-451b-a325-f175a71ea0ac/GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 13:04:24,336] [INFO] Query marker FASTA was written to GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:04:24,337] [INFO] Task started: Blastn
[2023-06-29 13:04:24,337] [INFO] Running command: blastn -query GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg922ff91f-2535-408f-9726-9c498aa70da8/dqc_reference/reference_markers.fasta -out GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:04:24,846] [INFO] Task succeeded: Blastn
[2023-06-29 13:04:24,851] [INFO] Selected 25 target genomes.
[2023-06-29 13:04:24,851] [INFO] Target genome list was writen to GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:04:24,857] [INFO] Task started: fastANI
[2023-06-29 13:04:24,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cb70099-15de-451b-a325-f175a71ea0ac/GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:04:42,735] [INFO] Task succeeded: fastANI
[2023-06-29 13:04:42,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg922ff91f-2535-408f-9726-9c498aa70da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:04:42,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg922ff91f-2535-408f-9726-9c498aa70da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:04:42,739] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:04:42,739] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:04:42,739] [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
--------------------------------------------------------------------------------
[2023-06-29 13:04:42,742] [INFO] DFAST Taxonomy check result was written to GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:04:42,742] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:04:42,743] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:04:42,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg922ff91f-2535-408f-9726-9c498aa70da8/dqc_reference/checkm_data
[2023-06-29 13:04:42,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:04:42,769] [INFO] Task started: CheckM
[2023-06-29 13:04:42,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:05:00,288] [INFO] Task succeeded: CheckM
[2023-06-29 13:05:00,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.65%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:05:00,311] [INFO] ===== Completeness check finished =====
[2023-06-29 13:05:00,311] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:05:00,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:05:00,312] [INFO] Task started: Blastn
[2023-06-29 13:05:00,312] [INFO] Running command: blastn -query GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg922ff91f-2535-408f-9726-9c498aa70da8/dqc_reference/reference_markers_gtdb.fasta -out GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:05:00,857] [INFO] Task succeeded: Blastn
[2023-06-29 13:05:00,862] [INFO] Selected 11 target genomes.
[2023-06-29 13:05:00,862] [INFO] Target genome list was writen to GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:05:00,870] [INFO] Task started: fastANI
[2023-06-29 13:05:00,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cb70099-15de-451b-a325-f175a71ea0ac/GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:05:05,060] [INFO] Task succeeded: fastANI
[2023-06-29 13:05:05,077] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:05:05,077] [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_018713375.1	s__Scatomorpha stercorigallinarum	97.8598	201	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018712985.1	s__Scatomorpha intestinavium	84.8994	183	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545405.1	s__Scatomorpha sp900545405	80.5123	144	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	98.32	98.22	0.88	0.84	4	-
GCA_018716005.1	s__Scatomorpha stercoravium	80.4818	102	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759385.1	s__Scatomorpha sp900759385	79.9864	130	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	98.68	98.63	0.90	0.88	3	-
GCA_900544765.1	s__Scatomorpha gallistercoris	79.9003	115	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	97.92	97.86	0.89	0.87	3	-
GCA_900546485.1	s__Scatomorpha sp900546485	79.7826	122	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543085.1	s__Scatomorpha pullicola	79.6208	125	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	97.83	97.68	0.88	0.83	7	-
GCA_900544295.1	s__Scatomorpha intestinigallinarum	79.2749	121	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.03	98.73	0.92	0.89	6	-
GCA_900752445.1	s__Scatomorpha sp900752445	79.0333	117	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.73	99.73	0.90	0.90	2	-
GCA_900546615.1	s__Scatomorpha pullistercoris	78.9415	102	226	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.45	98.95	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-29 13:05:05,079] [INFO] GTDB search result was written to GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:05:05,080] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:05:05,083] [INFO] DFAST_QC result json was written to GCA_937893095.1_SRR2134673_bin.50_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:05:05,083] [INFO] DFAST_QC completed!
[2023-06-29 13:05:05,083] [INFO] Total running time: 0h0m46s