[2023-06-19 10:56:01,080] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:56:01,085] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:56:01,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fbcc47e-7892-4ff6-85b3-16105e28eb66/dqc_reference
[2023-06-19 10:56:02,977] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:56:02,978] [INFO] Task started: Prodigal
[2023-06-19 10:56:02,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg577cfdb3-4e5e-4ac4-8eeb-89698ac7d12a/GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:56:09,352] [INFO] Task succeeded: Prodigal
[2023-06-19 10:56:09,353] [INFO] Task started: HMMsearch
[2023-06-19 10:56:09,353] [INFO] Running command: hmmsearch --tblout GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fbcc47e-7892-4ff6-85b3-16105e28eb66/dqc_reference/reference_markers.hmm GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:56:09,577] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:56:09,578] [INFO] Found 6/6 markers.
[2023-06-19 10:56:09,605] [INFO] Query marker FASTA was written to GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 10:56:09,605] [INFO] Task started: Blastn
[2023-06-19 10:56:09,605] [INFO] Running command: blastn -query GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fbcc47e-7892-4ff6-85b3-16105e28eb66/dqc_reference/reference_markers.fasta -out GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:10,270] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:10,275] [INFO] Selected 30 target genomes.
[2023-06-19 10:56:10,275] [INFO] Target genome list was writen to GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 10:56:10,278] [INFO] Task started: fastANI
[2023-06-19 10:56:10,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg577cfdb3-4e5e-4ac4-8eeb-89698ac7d12a/GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:56:27,371] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:27,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fbcc47e-7892-4ff6-85b3-16105e28eb66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:56:27,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fbcc47e-7892-4ff6-85b3-16105e28eb66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:56:27,375] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:56:27,375] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:56:27,375] [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
--------------------------------------------------------------------------------
[2023-06-19 10:56:27,378] [INFO] DFAST Taxonomy check result was written to GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 10:56:27,379] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:56:27,379] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:56:27,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fbcc47e-7892-4ff6-85b3-16105e28eb66/dqc_reference/checkm_data
[2023-06-19 10:56:27,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:56:27,418] [INFO] Task started: CheckM
[2023-06-19 10:56:27,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 10:56:51,374] [INFO] Task succeeded: CheckM
[2023-06-19 10:56:51,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:56:51,399] [INFO] ===== Completeness check finished =====
[2023-06-19 10:56:51,399] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:56:51,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 10:56:51,400] [INFO] Task started: Blastn
[2023-06-19 10:56:51,400] [INFO] Running command: blastn -query GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fbcc47e-7892-4ff6-85b3-16105e28eb66/dqc_reference/reference_markers_gtdb.fasta -out GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:52,546] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:52,551] [INFO] Selected 17 target genomes.
[2023-06-19 10:56:52,552] [INFO] Target genome list was writen to GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:56:52,581] [INFO] Task started: fastANI
[2023-06-19 10:56:52,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg577cfdb3-4e5e-4ac4-8eeb-89698ac7d12a/GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:57:00,185] [INFO] Task succeeded: fastANI
[2023-06-19 10:57:00,203] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 10:57:00,203] [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_900553525.1	s__UMGS1623 sp900553525	79.8335	260	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1623	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546265.1	s__UMGS856 sp900546265	78.0073	176	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS856	95.0	99.40	99.16	0.90	0.87	3	-
GCA_900760305.1	s__UMGS856 sp900760305	77.8885	134	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS856	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904377855.1	s__Avimonas merdigallinarum	77.7509	146	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904419875.1	s__Avimonas caecicola	77.5149	156	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCF_904419005.1	s__Avimonas faecium	77.4801	125	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	99.95	99.95	0.90	0.90	2	-
GCA_900761355.1	s__Avimonas intestinalis	77.338	139	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	99.06	98.52	0.89	0.88	4	-
GCA_900553255.1	s__UMGS1591 sp900553255	77.3226	123	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1591	95.0	100.00	100.00	0.98	0.98	2	-
GCA_905192745.1	s__Avimonas sp900551425	77.2717	128	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	99.85	99.85	0.95	0.95	2	-
GCA_905198295.1	s__UMGS1591 sp905198295	77.0397	108	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1591	95.0	98.68	98.68	0.86	0.86	2	-
GCA_900555705.1	s__UMGS1858 sp900555705	76.8862	54	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1858	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904395335.1	s__Avimonas_A narfia	76.8611	110	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766585.1	s__HGM12789 sp900766585	76.5281	69	728	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__HGM12789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:57:00,205] [INFO] GTDB search result was written to GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 10:57:00,206] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:57:00,209] [INFO] DFAST_QC result json was written to GCA_937950335.1_SRR5091531_bin.114_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 10:57:00,209] [INFO] DFAST_QC completed!
[2023-06-19 10:57:00,209] [INFO] Total running time: 0h0m59s